rs1517634

Variant names:

• chr2-223318767-G-A
• rs1517634

Your query was ambiguous. Multiple possible variants found:

• chr2-223318767-G-A
• chr2-223318767-G-T

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 0.733 in 152,070 control chromosomes in the GnomAD database, including 41,916 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 0.73 (41916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.733 AC: 111338 AN: 151952 Hom.: 41892 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.733 AC: 111405 AN: 152070 Hom.: 41916 Cov.: 32 AF XY: 0.719 AC XY: 53457 AN XY: 74324

African (AFR) AF: 0.848 AC: 35201 AN: 41498

American (AMR) AF: 0.550 AC: 8398 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2414 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2123 AN: 5170

South Asian (SAS) AF: 0.646 AC: 3108 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6526 AN: 10544

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51073 AN: 67988

Other (OTH) AF: 0.738 AC: 1560 AN: 2114

Alfa AF: 0.738 Hom.: 21156

Bravo AF: 0.731

Asia WGS AF: 0.570 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1517634; hg19: chr2-224183485;