rs1657855

Variant names:

• chr2-44917613-G-A
• rs1657855

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 0.176 in 152,000 control chromosomes in the GnomAD database, including 4,098 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 0.18 (4098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.176 AC: 26750 AN: 151882 Hom.: 4075 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.176 AC: 26814 AN: 152000 Hom.: 4098 Cov.: 32 AF XY: 0.175 AC XY: 12968 AN XY: 74310

African (AFR) AF: 0.408 AC: 16898 AN: 41392

American (AMR) AF: 0.163 AC: 2494 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1041 AN: 5164

South Asian (SAS) AF: 0.182 AC: 872 AN: 4804

European-Finnish (FIN) AF: 0.0374 AC: 396 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0621 AC: 4219 AN: 67988

Other (OTH) AF: 0.183 AC: 385 AN: 2108

Alfa AF: 0.101 Hom.: 5616

Bravo AF: 0.198

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs1657855; hg19: chr2-45144752;