rs1175861

Variant names:

• chr2-4176478-C-T
• rs1175861

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 0.557 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

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 = 0.967 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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.563

Alfa AF: 0.570 Hom.: 26884

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1175861; hg19: chr2-4224068;