dbSNP rs4901706: TMEM260:n.*1204G>A (chr14-56647667-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000539559.6(TMEM260):n.*1204G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 675,144 control chromosomes in the GnomAD database, including 3,491 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1449 hom., cov: 33)

Exomes 𝑓: 0.069 ( 2042 hom. )

Consequence

TMEM260
ENST00000539559.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

20 publications found

Variant links:

Genes affected

TMEM260 (HGNC:20185): (transmembrane protein 260) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM260 Gene-Disease associations (from GenCC):

structural heart defects and renal anomalies syndrome
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

TMEM260 links:

ENSG00000258428 (HGNC:):

ENSG00000258428 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM260	NM_017799.4 link	c.*170G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000261556.11	NP_060269.3	Q9NX78-1B3KN73

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM260	ENST00000261556.11 link	c.*170G>A		3_prime_UTR_variant	Exon 16 of 16	2	NM_017799.4	ENSP00000261556.6		Q9NX78-1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17230

AN:

152008

Hom.:

1439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.0831

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.0708

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0479

Gnomad OTH

AF:

0.0898

GnomAD4 exome

AF:

0.0686

AC:

35866

AN:

523018

Hom.:

2042

Cov.:

AF XY:

0.0676

AC XY:

18104

AN XY:

267798

show subpopulations

African (AFR)

AF:

0.195

AC:

2253

AN:

11572

American (AMR)

AF:

0.181

AC:

2182

AN:

12036

Ashkenazi Jewish (ASJ)

AF:

0.0758

AC:

992

AN:

13090

East Asian (EAS)

AF:

0.246

AC:

6602

AN:

26892

South Asian (SAS)

AF:

0.0687

AC:

2505

AN:

36472

European-Finnish (FIN)

AF:

0.101

AC:

2817

AN:

27830

Middle Eastern (MID)

AF:

0.0713

AC:

151

AN:

2118

European-Non Finnish (NFE)

AF:

0.0438

AC:

16020

AN:

365490

Other (OTH)

AF:

0.0852

AC:

2344

AN:

27518

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1531

3061

4592

6122

7653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.113

AC:

17262

AN:

152126

Hom.:

1449

Cov.:

AF XY:

0.117

AC XY:

8682

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.195

AC:

8099

AN:

41488

American (AMR)

AF:

0.153

AC:

2339

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0831

AC:

288

AN:

3464

East Asian (EAS)

AF:

0.298

AC:

1540

AN:

5170

South Asian (SAS)

AF:

0.0701

AC:

338

AN:

4824

European-Finnish (FIN)

AF:

0.109

AC:

1155

AN:

10582

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0478

AC:

3253

AN:

67994

Other (OTH)

AF:

0.0907

AC:

192

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

749

1498

2246

2995

3744

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.0740

Hom.:

993

Bravo

AF:

0.123

Asia WGS

AF:

0.190

AC:

659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.15

(source)

DANN

Benign

0.47

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism (auto)

(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

Computational scores

Splicing

Publications

Other links and lift over