11-63411915-T-A

Variant names:

• chr11-63411915-T-A
• rs637122

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 0.484 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.823 AC: 33648 AN: 40902

American (AMR) AF: 0.503 AC: 7541 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3450

East Asian (EAS) AF: 0.820 AC: 4197 AN: 5116

South Asian (SAS) AF: 0.487 AC: 2314 AN: 4748

European-Finnish (FIN) AF: 0.315 AC: 2883 AN: 9162

Middle Eastern (MID) AF: 0.277 AC: 78 AN: 282

European-Non Finnish (NFE) AF: 0.288 AC: 19343 AN: 67234

Other (OTH) AF: 0.471 AC: 977 AN: 2074

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs637122; hg19: chr11-63179387;