rs867563

chr2-136384930-A-Gchr2-136384930-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;