rs1955337

Variant names:

• chr2-168272635-G-T
• rs1955337

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 0.155 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.186 AC: 7721 AN: 41476

American (AMR) AF: 0.201 AC: 3079 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1635 AN: 5158

South Asian (SAS) AF: 0.192 AC: 925 AN: 4818

European-Finnish (FIN) AF: 0.0969 AC: 1026 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8436 AN: 67978

Other (OTH) AF: 0.167 AC: 353 AN: 2108

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1955337; hg19: chr2-169129145;