rs2215496

Variant names:

• chr17-5743244-A-G
• rs2215496

Your query was ambiguous. Multiple possible variants found:

• chr17-5743244-A-G
• chr17-5743244-A-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 0.485 in 151,584 control chromosomes in the GnomAD database, including 18,031 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 0.49 (18031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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 (AMR) allele frequency at 95% confidence interval = 0.521 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: 0.485 AC: 73521 AN: 151464 Hom.: 18012 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.485 AC: 73591 AN: 151584 Hom.: 18031 Cov.: 31 AF XY: 0.483 AC XY: 35782 AN XY: 74036

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.502

Alfa AF: 0.478 Hom.: 28678

Bravo AF: 0.490

Asia WGS AF: 0.385 AC: 1326 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215496; hg19: chr17-5646564;