rs1177274

Variant names:

• chr2-61141397-T-G
• rs1177274
• ENST00000462959.2:n.616+7121T>G

Variant summary

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

The ENST00000462959.2(ENSG00000274769):​n.616+7121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,026 control chromosomes in the GnomAD database, including 24,751 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 0.57 (24751 hom., cov: 32)
• Consequence: ENSG00000274769 ENST00000462959.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 19 publications found

Genes affected

ENSG00000274769 (HGNC:):

C2orf74-AS1 (HGNC:56377): (C2orf74 antisense RNA 1)

C2orf74-DT (HGNC:27941): (C2orf74 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C2orf74-DT	NR_036496.1	n.*195A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000274769	ENST00000462959.2	n.616+7121T>G		intron_variant	Intron 5 of 7	2
C2orf74-AS1	ENST00000420918.4	n.*195A>C		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86465 AN: 151908 Hom.: 24731 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.569 AC: 86525 AN: 152026 Hom.: 24751 Cov.: 32 AF XY: 0.575 AC XY: 42711 AN XY: 74314

African (AFR) AF: 0.514 AC: 21317 AN: 41464

American (AMR) AF: 0.613 AC: 9342 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.633 AC: 3273 AN: 5172

South Asian (SAS) AF: 0.598 AC: 2879 AN: 4818

European-Finnish (FIN) AF: 0.610 AC: 6446 AN: 10564

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38774 AN: 67980

Other (OTH) AF: 0.612 AC: 1289 AN: 2106

Alfa AF: 0.572 Hom.: 45806

Bravo AF: 0.570

Asia WGS AF: 0.584 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.62
DANN	Benign	0.43
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1177274; hg19: chr2-61368532;