rs200789033

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_181711.4(TAMALIN):c.1084G>A(p.Gly362Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,553,592 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0070 ( 7 hom., cov: 32)

Exomes 𝑓: 0.011 ( 98 hom. )

Consequence

TAMALIN
NM_181711.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.947

Publications

2 publications found

Variant links:

Genes affected

TAMALIN (HGNC:18707): (trafficking regulator and scaffold protein tamalin) This gene encodes a protein that functions as a molecular scaffold, linking receptors, including group 1 metabotropic glutamate receptors, to neuronal proteins. The encoded protein contains conserved domains, including a leucine zipper sequence, PDZ domain and a C-terminal PDZ-binding motif. Alternately spliced transcript variants have been observed for this gene.[provided by RefSeq, Dec 2012]

TAMALIN links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005762309).

BP6

Variant 12-52015095-G-A is Benign according to our data. Variant chr12-52015095-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 221938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAMALIN	NM_181711.4 link	c.1084G>A	p.Gly362Ser	missense_variant	Exon 8 of 8	ENST00000293662.9	NP_859062.1	Q7Z6J2-1
TAMALIN	NM_001271856.2 link	c.655G>A	p.Gly219Ser	missense_variant	Exon 7 of 7		NP_001258785.1	Q7Z6J2-2
TAMALIN	XM_005268691.4 link	c.694G>A	p.Gly232Ser	missense_variant	Exon 8 of 8		XP_005268748.1
TAMALIN	XM_047428439.1 link	c.694G>A	p.Gly232Ser	missense_variant	Exon 7 of 7		XP_047284395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAMALIN	ENST00000293662.9 link	c.1084G>A	p.Gly362Ser	missense_variant	Exon 8 of 8	1	NM_181711.4	ENSP00000293662.4		Q7Z6J2-1

Frequencies

GnomAD3 genomes

AF:

0.00699

AC:

1057

AN:

151286

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00335

Gnomad ASJ

AF:

0.00579

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.00482

GnomAD2 exomes

AF:

0.00635

AC:

1006

AN:

158510

AF XY:

0.00661

show subpopulations

Gnomad AFR exome

AF:

0.00125

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.00728

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00941

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00530

GnomAD4 exome

AF:

0.0108

AC:

15175

AN:

1402196

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

7325

AN XY:

695192

show subpopulations

African (AFR)

AF:

0.00133

AC:

AN:

31688

American (AMR)

AF:

0.00194

AC:

AN:

37614

Ashkenazi Jewish (ASJ)

AF:

0.00777

AC:

194

AN:

24968

East Asian (EAS)

AF:

0.00

AC:

AN:

36914

South Asian (SAS)

AF:

0.00494

AC:

404

AN:

81782

European-Finnish (FIN)

AF:

0.00848

AC:

295

AN:

34792

Middle Eastern (MID)

AF:

0.00110

AC:

AN:

5470

European-Non Finnish (NFE)

AF:

0.0125

AC:

13611

AN:

1090490

Other (OTH)

AF:

0.00941

AC:

550

AN:

58478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

724

1447

2171

2894

3618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

526

1052

1578

2104

2630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00698

AC:

1057

AN:

151396

Hom.:

Cov.:

AF XY:

0.00649

AC XY:

480

AN XY:

73934

show subpopulations

African (AFR)

AF:

0.00174

AC:

AN:

41452

American (AMR)

AF:

0.00335

AC:

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.00579

AC:

AN:

3452

East Asian (EAS)

AF:

0.00

AC:

AN:

5144

South Asian (SAS)

AF:

0.00311

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.0117

AC:

121

AN:

10374

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0112

AC:

759

AN:

67616

Other (OTH)

AF:

0.00477

AC:

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

104

155

207

259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00824

Hom.:

Bravo

AF:

0.00651

ESP6500AA

AF:

0.00255

AC:

ESP6500EA

AF:

0.00619

AC:

ExAC

AF:

0.00544

AC:

617

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

TAMALIN: BS1, BS2 -

Anophthalmia-microphthalmia syndrome

Benign:1

Jan 01, 2013

Paul Sabatier University EA-4555, Paul Sabatier University

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.20

T;.

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.36

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.71

T;T

MetaRNN

Benign

0.0058

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.4

L;.

PhyloP100

0.95

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-0.77

N;N

REVEL

Benign

0.10

Sift

Benign

0.082

T;D

Sift4G

Pathogenic

0.0

D;D

Polyphen

0.66

P;P

Vest4

0.14

MVP

0.68

MPC

1.9

ClinPred

0.0051

GERP RS

3.8

Varity_R

0.069

gMVP

0.38

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over