rs6756192

Variant names:

• chr2-119366128-C-T
• rs6756192
• NM_001322331.2:c.-13+662G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322331.2(C2orf76):​c.-13+662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,950 control chromosomes in the GnomAD database, including 2,459 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 (2459 hom., cov: 32)
• Consequence: C2orf76 NM_001322331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 10 publications found

Genes affected

C2orf76 (HGNC:27017): (chromosome 2 open reading frame 76)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C2orf76	NM_001322331.2	c.-13+662G>A		intron_variant	Intron 1 of 5	ENST00000334816.12	NP_001309260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf76	ENST00000334816.12	c.-13+662G>A		intron_variant	Intron 1 of 5	1	NM_001322331.2	ENSP00000335041.7

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26280 AN: 151832 Hom.: 2458 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.173 AC: 26296 AN: 151950 Hom.: 2459 Cov.: 32 AF XY: 0.171 AC XY: 12678 AN XY: 74266

African (AFR) AF: 0.135 AC: 5607 AN: 41416

American (AMR) AF: 0.159 AC: 2435 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5156

South Asian (SAS) AF: 0.136 AC: 656 AN: 4812

European-Finnish (FIN) AF: 0.155 AC: 1632 AN: 10530

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13814 AN: 67982

Other (OTH) AF: 0.153 AC: 323 AN: 2110

Alfa AF: 0.192 Hom.: 11060

Bravo AF: 0.171

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		-0.014
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs6756192; hg19: chr2-120123704; COSMIC: COSV58346020; COSMIC: COSV58346020;