Variant 17-8173337-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_183065.4(TMEM107):c.*866G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 575,800 control chromosomes in the GnomAD database, including 30,702 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 6497 hom., cov: 33)

Exomes 𝑓: 0.32 ( 24205 hom. )

Consequence

TMEM107
NM_183065.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.28

Variant links:

Genes affected

TMEM107 (HGNC:28128): (transmembrane protein 107) This gene encodes a transmembrane protein and component of the primary cilia transition zone. The encoded protein regulates ciliogenesis and ciliary protein composition. Human fibroblasts expressing a mutant allele of this gene exhibit reduced numbers of cilia, altered cilia length, and impaired sonic hedgehog signaling. In human patients, different mutations in this gene cause different ciliopathies, including Meckel-Gruber syndrome and orofaciodigital syndrome. [provided by RefSeq, May 2017]

TMEM107 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 17-8173337-C-T is Benign according to our data. Variant chr17-8173337-C-T is described in ClinVar as [Benign]. Clinvar id is 1294573.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM107	NM_183065.4 linkuse as main transcript	c.*866G>A		3_prime_UTR_variant	5/5	ENST00000437139.7	NP_898888.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM107	ENST00000437139.7 linkuse as main transcript	c.*866G>A		3_prime_UTR_variant	5/5	1	NM_183065.4	ENSP00000402732	P1	Q6UX40-1
TMEM107	ENST00000449985.6 linkuse as main transcript	c.*915G>A		3_prime_UTR_variant	2/2	1		ENSP00000404753

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40229

AN:

151782

Hom.:

6500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0963

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.321

AC:

135943

AN:

423900

Hom.:

24205

Cov.:

AF XY:

0.319

AC XY:

72467

AN XY:

227160

show subpopulations

Gnomad4 AFR exome

AF:

0.0921

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.264

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.406

Gnomad4 NFE exome

AF:

0.379

Gnomad4 OTH exome

AF:

0.313

GnomAD4 genome

AF:

0.265

AC:

40218

AN:

151900

Hom.:

6497

Cov.:

AF XY:

0.261

AC XY:

19392

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.0961

Gnomad4 AMR

AF:

0.199

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.116

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.402

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.340

Hom.:

10180

Bravo

AF:

0.242

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 09, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.31

DANN

Benign

0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over