rs6670793

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000373954.11(FAM76A):ā€‹c.234A>Gā€‹(p.Ala78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 1,609,970 control chromosomes in the GnomAD database, including 13,298 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: š‘“ 0.17 ( 6044 hom., cov: 32)
Exomes š‘“: 0.042 ( 7254 hom. )

Consequence

FAM76A
ENST00000373954.11 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.658
Variant links:
Genes affected
FAM76A (HGNC:28530): (family with sequence similarity 76 member A) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP7
Synonymous conserved (PhyloP=-0.658 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM76ANM_152660.3 linkuse as main transcriptc.234A>G p.Ala78= synonymous_variant 4/9 ENST00000373954.11 NP_689873.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM76AENST00000373954.11 linkuse as main transcriptc.234A>G p.Ala78= synonymous_variant 4/91 NM_152660.3 ENSP00000363065 P1Q8TAV0-1

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
26261
AN:
151940
Hom.:
6010
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.524
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0856
Gnomad ASJ
AF:
0.0478
Gnomad EAS
AF:
0.253
Gnomad SAS
AF:
0.104
Gnomad FIN
AF:
0.00226
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0153
Gnomad OTH
AF:
0.128
GnomAD3 exomes
AF:
0.0846
AC:
20929
AN:
247352
Hom.:
3316
AF XY:
0.0755
AC XY:
10085
AN XY:
133622
show subpopulations
Gnomad AFR exome
AF:
0.542
Gnomad AMR exome
AF:
0.0553
Gnomad ASJ exome
AF:
0.0458
Gnomad EAS exome
AF:
0.270
Gnomad SAS exome
AF:
0.0990
Gnomad FIN exome
AF:
0.00403
Gnomad NFE exome
AF:
0.0157
Gnomad OTH exome
AF:
0.0498
GnomAD4 exome
AF:
0.0418
AC:
60922
AN:
1457912
Hom.:
7254
Cov.:
31
AF XY:
0.0418
AC XY:
30339
AN XY:
725090
show subpopulations
Gnomad4 AFR exome
AF:
0.544
Gnomad4 AMR exome
AF:
0.0585
Gnomad4 ASJ exome
AF:
0.0465
Gnomad4 EAS exome
AF:
0.230
Gnomad4 SAS exome
AF:
0.0985
Gnomad4 FIN exome
AF:
0.00448
Gnomad4 NFE exome
AF:
0.0149
Gnomad4 OTH exome
AF:
0.0752
GnomAD4 genome
AF:
0.173
AC:
26346
AN:
152058
Hom.:
6044
Cov.:
32
AF XY:
0.170
AC XY:
12675
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.524
Gnomad4 AMR
AF:
0.0855
Gnomad4 ASJ
AF:
0.0478
Gnomad4 EAS
AF:
0.254
Gnomad4 SAS
AF:
0.103
Gnomad4 FIN
AF:
0.00226
Gnomad4 NFE
AF:
0.0153
Gnomad4 OTH
AF:
0.127
Alfa
AF:
0.0479
Hom.:
2101
Bravo
AF:
0.196
Asia WGS
AF:
0.164
AC:
568
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
3.0
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs6670793; hg19: chr1-28060574; COSMIC: COSV50549105; API