rs1657855

Positions:

• chr2-44917613-G-A

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 0.176 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0621

Gnomad4 OTH AF: 0.183

Alfa AF: 0.0824 Hom.: 1364

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1657855; hg19: chr2-45144752;