Variant chr10-14667659-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_031453.4(FAM107B):c.444C>T(p.Leu148=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00371 in 1,614,062 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0036 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 107 hom. )

Consequence

FAM107B
NM_031453.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.02

Variant links:

Genes affected

FAM107B (HGNC:23726): (family with sequence similarity 107 member B) Predicted to act upstream of or within sensory perception of sound. [provided by Alliance of Genome Resources, Apr 2022]

FAM107B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 10-14667659-G-A is Benign according to our data. Variant chr10-14667659-G-A is described in ClinVar as [Benign]. Clinvar id is 781937.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.02 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00363 (553/152276) while in subpopulation EAS AF= 0.0522 (271/5194). AF 95% confidence interval is 0.0471. There are 11 homozygotes in gnomad4. There are 326 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107B	NM_031453.4 linkuse as main transcript	c.444C>T	p.Leu148=	synonymous_variant	2/5	ENST00000181796.7
FAM107B	NM_001282695.2 linkuse as main transcript	c.-148C>T		5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7 linkuse as main transcript	c.444C>T	p.Leu148=	synonymous_variant	2/5	2	NM_031453.4		Q9H098-2
FAM107B	ENST00000487335.5 linkuse as main transcript	c.444C>T	p.Leu148=	synonymous_variant, NMD_transcript_variant	2/6	1

Frequencies

GnomAD3 genomes

AF:

0.00366

AC:

557

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000555

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.0526

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000603

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00865

AC:

2174

AN:

251362

Hom.:

AF XY:

0.00905

AC XY:

1230

AN XY:

135858

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.0114

Gnomad EAS exome

AF:

0.0560

Gnomad SAS exome

AF:

0.0273

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000607

Gnomad OTH exome

AF:

0.00587

GnomAD4 exome

AF:

0.00372

AC:

5442

AN:

1461786

Hom.:

107

Cov.:

AF XY:

0.00440

AC XY:

3202

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00237

Gnomad4 ASJ exome

AF:

0.0106

Gnomad4 EAS exome

AF:

0.0406

Gnomad4 SAS exome

AF:

0.0275

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.000567

Gnomad4 OTH exome

AF:

0.00654

GnomAD4 genome

AF:

0.00363

AC:

553

AN:

152276

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

326

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.000553

Gnomad4 AMR

AF:

0.00163

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.0522

Gnomad4 SAS

AF:

0.0315

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000588

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00146

Hom.:

Bravo

AF:

0.00363

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.000872

EpiControl

AF:

0.000948

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	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.28

DANN

Benign

0.71

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