11-20540973-C-T

Position:

• chr11-20540973-C-T

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 0.969 in 152,312 control chromosomes in the GnomAD database, including 72,006 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 0.97 (72006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147556 AN: 152194 Hom.: 71957 Cov.: 32

Gnomad AFR AF: 0.994

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.969 AC: 147663 AN: 152312 Hom.: 72006 Cov.: 32 AF XY: 0.966 AC XY: 71945 AN XY: 74470

Gnomad4 AFR AF: 0.994

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.965

Alfa AF: 0.973 Hom.: 86306

Bravo AF: 0.959

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7128311; hg19: chr11-20562519;