11-636496-A-G

Variant names:

• chr11-636496-A-G
• rs936461

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 0.555 in 152,010 control chromosomes in the GnomAD database, including 24,824 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 0.56 (24824 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.555 AC: 84369 AN: 151892 Hom.: 24826 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.555 AC: 84395 AN: 152010 Hom.: 24824 Cov.: 33 AF XY: 0.558 AC XY: 41493 AN XY: 74336

African (AFR) AF: 0.349 AC: 14445 AN: 41434

American (AMR) AF: 0.502 AC: 7662 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2145 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3813 AN: 5150

South Asian (SAS) AF: 0.580 AC: 2797 AN: 4824

European-Finnish (FIN) AF: 0.701 AC: 7425 AN: 10596

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 43997 AN: 67946

Other (OTH) AF: 0.586 AC: 1238 AN: 2114

Alfa AF: 0.551 Hom.: 13074

Bravo AF: 0.532

Asia WGS AF: 0.608 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.96
DANN	Benign	0.23
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs936461; hg19: chr11-636496;