chr2-119365701-C-T

Position:

• chr2-119365701-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322331.2(C2orf76):​c.-13+1089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,016 control chromosomes in the GnomAD database, including 6,569 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 0.29 (6569 hom., cov: 32)
• Consequence: C2orf76 NM_001322331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf76	NM_001322331.2	c.-13+1089G>A		intron_variant		ENST00000334816.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf76	ENST00000334816.12	c.-13+1089G>A		intron_variant		1	NM_001322331.2	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44063 AN: 151898 Hom.: 6557 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.290 AC: 44110 AN: 152016 Hom.: 6569 Cov.: 32 AF XY: 0.289 AC XY: 21453 AN XY: 74296

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.254

Alfa AF: 0.285 Hom.: 10686

Bravo AF: 0.289

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs11693629; hg19: chr2-120123277; COSMIC: COSV58346017; COSMIC: COSV58346017;