Variant 13-51251598-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_001242312.2(FAM124A):c.231G>A(p.Pro77Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00254 in 1,569,220 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 37 hom., cov: 33)

Exomes 𝑓: 0.0015 ( 36 hom. )

Consequence

FAM124A
NM_001242312.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.502

Variant links:

Genes affected

FAM124A (HGNC:26413): (family with sequence similarity 124 member A)

FAM124A 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=-0.49).

BP6

Variant 13-51251598-G-A is Benign according to our data. Variant chr13-51251598-G-A is described in ClinVar as [Benign]. Clinvar id is 787411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.502 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1817/152314) while in subpopulation AFR AF= 0.0412 (1712/41570). AF 95% confidence interval is 0.0396. There are 37 homozygotes in gnomad4. There are 858 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 37 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM124A	NM_001242312.2 linkuse as main transcript	c.231G>A	p.Pro77Pro	synonymous_variant	3/4	ENST00000322475.13	NP_001229241.1	Q86V42-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FAM124A	ENST00000322475.13 linkuse as main transcript	c.231G>A	p.Pro77Pro	synonymous_variant	3/4	1	NM_001242312.2	ENSP00000324625.8	Q86V42-1
FAM124A	ENST00000615498.4 linkuse as main transcript	c.231G>A	p.Pro77Pro	synonymous_variant	3/3	1		ENSP00000481212.1	Q86V42-3
FAM124A	ENST00000280057.6 linkuse as main transcript	c.339G>A	p.Pro113Pro	synonymous_variant	4/5	2		ENSP00000280057.6	Q86V42-2

Frequencies

GnomAD3 genomes

AF:

0.0119

AC:

1813

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0412

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00425

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00369

AC:

798

AN:

216476

Hom.:

AF XY:

0.00267

AC XY:

311

AN XY:

116338

show subpopulations

Gnomad AFR exome

AF:

0.0447

Gnomad AMR exome

AF:

0.00219

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00120

Gnomad NFE exome

AF:

0.000204

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00153

AC:

2173

AN:

1416906

Hom.:

Cov.:

AF XY:

0.00138

AC XY:

962

AN XY:

698554

show subpopulations

Gnomad4 AFR exome

AF:

0.0482

Gnomad4 AMR exome

AF:

0.00245

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000101

Gnomad4 FIN exome

AF:

0.000944

Gnomad4 NFE exome

AF:

0.000193

Gnomad4 OTH exome

AF:

0.00378

GnomAD4 genome

AF:

0.0119

AC:

1817

AN:

152314

Hom.:

Cov.:

AF XY:

0.0115

AC XY:

858

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0412

Gnomad4 AMR

AF:

0.00425

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00675

Hom.:

Bravo

AF:

0.0142

Asia WGS

AF:

0.00115

AC:

AN:

3478

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	Nov 16, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

6.5

DANN

Benign

0.88

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

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