11-58626681-C-T

Variant names:

• chr11-58626681-C-T
• rs550942

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 0.884 in 152,296 control chromosomes in the GnomAD database, including 59,871 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 0.88 (59871 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 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: 0.884 AC: 134532 AN: 152178 Hom.: 59812 Cov.: 33

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.884 AC: 134649 AN: 152296 Hom.: 59871 Cov.: 33 AF XY: 0.888 AC XY: 66087 AN XY: 74456

African (AFR) AF: 0.969 AC: 40283 AN: 41574

American (AMR) AF: 0.917 AC: 14027 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3018 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3734 AN: 5184

South Asian (SAS) AF: 0.905 AC: 4364 AN: 4824

European-Finnish (FIN) AF: 0.910 AC: 9655 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56619 AN: 68016

Other (OTH) AF: 0.894 AC: 1888 AN: 2112

Alfa AF: 0.859 Hom.: 102828

Bravo AF: 0.887

Asia WGS AF: 0.841 AC: 2923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.25
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs550942; hg19: chr11-58394154;