rs867563

Variant names:

• chr2-136384930-A-G
• rs867563

Your query was ambiguous. Multiple possible variants found:

• chr2-136384930-A-G
• chr2-136384930-A-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 0.268 in 151,632 control chromosomes in the GnomAD database, including 5,585 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 0.27 (5585 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40594 AN: 151512 Hom.: 5578 Cov.: 30

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.268 AC: 40640 AN: 151632 Hom.: 5585 Cov.: 30 AF XY: 0.270 AC XY: 19973 AN XY: 74030

African (AFR) AF: 0.205 AC: 8478 AN: 41346

American (AMR) AF: 0.308 AC: 4683 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1921 AN: 5086

South Asian (SAS) AF: 0.298 AC: 1433 AN: 4810

European-Finnish (FIN) AF: 0.323 AC: 3384 AN: 10462

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19157 AN: 67922

Other (OTH) AF: 0.261 AC: 550 AN: 2108

Alfa AF: 0.276 Hom.: 772

Bravo AF: 0.265

Asia WGS AF: 0.348 AC: 1209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.46
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs867563; hg19: chr2-137142500;