rs11888528

chr2-119361188-T-C

Variant summary

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

The NM_001322331.2(C2orf76):c.-13+5602A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,174 control chromosomes in the GnomAD database, including 9,948 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 0.36 (9948 hom., cov: 33)
• Consequence: C2orf76 NM_001322331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf76	NM_001322331.2	c.-13+5602A>G		intron_variant		ENST00000334816.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf76	ENST00000334816.12	c.-13+5602A>G		intron_variant		1	NM_001322331.2	P1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54485 AN: 152056 Hom.: 9938 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.358 AC: 54528 AN: 152174 Hom.: 9948 Cov.: 33 AF XY: 0.354 AC XY: 26340 AN XY: 74392

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.331

Alfa AF: 0.369 Hom.: 1651

Bravo AF: 0.358

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.80
Dann	Benign	0.30

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: rs11888528; hg19: chr2-120118764; COSMIC: COSV58345974;