rs1955337

Positions:

• chr2-168272635-G-T

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 0.155 in 152,104 control chromosomes in the GnomAD database, including 1,985 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 0.16 (1985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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: 0.155 AC: 23559 AN: 151986 Hom.: 1984 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0969

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.155 AC: 23579 AN: 152104 Hom.: 1985 Cov.: 32 AF XY: 0.155 AC XY: 11493 AN XY: 74368

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0969

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.167

Alfa AF: 0.134 Hom.: 409

Bravo AF: 0.166

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1955337; hg19: chr2-169129145;