11-36990987-A-T

Variant names:

• chr11-36990987-A-T
• rs391317

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 0.681 in 152,072 control chromosomes in the GnomAD database, including 36,984 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 0.68 (36984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.681 AC: 103498 AN: 151954 Hom.: 36974 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.681 AC: 103553 AN: 152072 Hom.: 36984 Cov.: 33 AF XY: 0.686 AC XY: 50968 AN XY: 74322

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.715

Alfa AF: 0.749 Hom.: 23821

Bravo AF: 0.673

Asia WGS AF: 0.720 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs391317; hg19: chr11-37012537;