rs6670793

Variant names:

• chr1-27734063-A-G
• rs6670793
• NM_152660.3:c.234A>G
• FAM76A p.Ala78Ala

Your query was ambiguous. Multiple possible variants found:

• chr1-27734063-A-G
• chr1-27734063-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_152660.3(FAM76A):​c.234A>G​(p.Ala78Ala) 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: 𝑓 0.17 (6044 hom., cov: 32)
  • Exomes 𝑓: 0.042 (7254 hom.)
• Consequence: FAM76A NM_152660.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152660.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM76A	NM_152660.3	MANE Select	c.234A>G	p.Ala78Ala	synonymous	Exon 4 of 9	NP_689873.1	Q8TAV0-1
	FAM76A	NM_001143912.2		c.336A>G	p.Ala112Ala	synonymous	Exon 5 of 10	NP_001137384.1	Q8TAV0-3
	FAM76A	NM_001143913.2		c.336A>G	p.Ala112Ala	synonymous	Exon 5 of 9	NP_001137385.1	Q8TAV0-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM76A	ENST00000373954.11	TSL:1 MANE Select	c.234A>G	p.Ala78Ala	synonymous	Exon 4 of 9	ENSP00000363065.5	Q8TAV0-1
	FAM76A	ENST00000010299.10	TSL:1	c.336A>G	p.Ala112Ala	synonymous	Exon 5 of 10	ENSP00000010299.6	Q8TAV0-3
	FAM76A	ENST00000234549.11	TSL:1	c.336A>G	p.Ala112Ala	synonymous	Exon 5 of 9	ENSP00000234549.7	Q8TAV0-4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26261 AN: 151940 Hom.: 6010 Cov.: 32

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

GnomAD2 exomes AF: 0.0846 AC: 20929 AN: 247352 AF XY: 0.0755

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 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

African (AFR) AF: 0.544 AC: 17953 AN: 33014

American (AMR) AF: 0.0585 AC: 2555 AN: 43654

Ashkenazi Jewish (ASJ) AF: 0.0465 AC: 1212 AN: 26062

East Asian (EAS) AF: 0.230 AC: 9106 AN: 39532

South Asian (SAS) AF: 0.0985 AC: 8372 AN: 84968

European-Finnish (FIN) AF: 0.00448 AC: 239 AN: 53402

Middle Eastern (MID) AF: 0.0710 AC: 409 AN: 5762

European-Non Finnish (NFE) AF: 0.0149 AC: 16545 AN: 1111274

Other (OTH) AF: 0.0752 AC: 4531 AN: 60244

GnomAD4 genome AF: 0.173 AC: 26346 AN: 152058 Hom.: 6044 Cov.: 32 AF XY: 0.170 AC XY: 12675 AN XY: 74342

African (AFR) AF: 0.524 AC: 21702 AN: 41400

American (AMR) AF: 0.0855 AC: 1305 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5166

South Asian (SAS) AF: 0.103 AC: 499 AN: 4822

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1042 AN: 68004

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.0680 Hom.: 7759

Bravo AF: 0.196

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		-0.66
Mutation Taster		=97/3	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6670793;

hg19: chr1-28060574;

COSMIC: COSV50549105;