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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.268 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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.261

Alfa AF: 0.278 Hom.: 746

Bravo AF: 0.265

Asia WGS AF: 0.348 AC: 1209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867563; hg19: chr2-137142500;