rs637122

chr11-63411915-T-Achr11-63411915-T-C

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 0.484 in 148,858 control chromosomes in the GnomAD database, including 21,739 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 0.48 (21739 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.484 AC: 71942 AN: 148762 Hom.: 21687 Cov.: 29

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.484 AC: 72054 AN: 148858 Hom.: 21739 Cov.: 29 AF XY: 0.485 AC XY: 35183 AN XY: 72540

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.471

Alfa AF: 0.175 Hom.: 333

Bravo AF: 0.516

Asia WGS AF: 0.660 AC: 2261 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs637122; hg19: chr11-63179387;