chr11-36480237-A-T

Variant names:

• chr11-36480237-A-T
• rs331463

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 0.756 in 152,050 control chromosomes in the GnomAD database, including 45,249 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 0.76 (45249 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.756 AC: 114892 AN: 151932 Hom.: 45251 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.756 AC: 114912 AN: 152050 Hom.: 45249 Cov.: 31 AF XY: 0.760 AC XY: 56440 AN XY: 74310

African (AFR) AF: 0.509 AC: 21061 AN: 41410

American (AMR) AF: 0.863 AC: 13198 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2886 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4855 AN: 5166

South Asian (SAS) AF: 0.818 AC: 3938 AN: 4816

European-Finnish (FIN) AF: 0.814 AC: 8611 AN: 10576

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57612 AN: 67994

Other (OTH) AF: 0.787 AC: 1662 AN: 2112

Alfa AF: 0.789 Hom.: 5995

Bravo AF: 0.751

Asia WGS AF: 0.863 AC: 3001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs331463; hg19: chr11-36501787;