rs1177274

Positions:

• chr2-61141397-T-G

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.612

Alfa AF: 0.573 Hom.: 11514

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1177274; hg19: chr2-61368532;