rs1517635

Variant names:

• chr2-223338397-T-A
• rs1517635

Your query was ambiguous. Multiple possible variants found:

• chr2-223338397-T-A
• chr2-223338397-T-G

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 0.575 in 151,950 control chromosomes in the GnomAD database, including 25,756 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 0.58 (25756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.97
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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: 0.575 AC: 87325 AN: 151832 Hom.: 25730 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.575 AC: 87398 AN: 151950 Hom.: 25756 Cov.: 31 AF XY: 0.565 AC XY: 41953 AN XY: 74248

African (AFR) AF: 0.667 AC: 27636 AN: 41424

American (AMR) AF: 0.423 AC: 6457 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2034 AN: 5142

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4822

European-Finnish (FIN) AF: 0.507 AC: 5353 AN: 10560

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39487 AN: 67962

Other (OTH) AF: 0.579 AC: 1222 AN: 2110

Alfa AF: 0.561 Hom.: 2909

Bravo AF: 0.574

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.078
DANN	Benign	0.39
PhyloP100		-6.0

Splicing

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

Other links and lift over

dbSNP: rs1517635; hg19: chr2-224203115;