rs1175861

Variant names:

• chr2-4176478-C-T
• rs1175861

Variant summary

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

The variant allele was found at a frequency of 0.557 in 151,854 control chromosomes in the GnomAD database, including 24,723 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 0.56 (24723 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 5 publications found

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 = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84527 AN: 151736 Hom.: 24714 Cov.: 30

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.557 AC: 84567 AN: 151854 Hom.: 24723 Cov.: 30 AF XY: 0.563 AC XY: 41796 AN XY: 74220

African (AFR) AF: 0.415 AC: 17149 AN: 41338

American (AMR) AF: 0.660 AC: 10071 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5117 AN: 5170

South Asian (SAS) AF: 0.657 AC: 3158 AN: 4808

European-Finnish (FIN) AF: 0.610 AC: 6440 AN: 10554

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38581 AN: 67940

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.567 Hom.: 33323

Bravo AF: 0.557

Asia WGS AF: 0.789 AC: 2745 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	0.027
DANN	Benign	0.60
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs1175861; hg19: chr2-4224068;