11-93566577-G-T

Variant names:

• chr11-93566577-G-T
• rs7124828

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 0.15 in 152,200 control chromosomes in the GnomAD database, including 1,758 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 0.15 (1758 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 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: 0.150 AC: 22807 AN: 152082 Hom.: 1756 Cov.: 34

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.150 AC: 22812 AN: 152200 Hom.: 1758 Cov.: 34 AF XY: 0.147 AC XY: 10972 AN XY: 74420

African (AFR) AF: 0.122 AC: 5083 AN: 41528

American (AMR) AF: 0.107 AC: 1633 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3468

East Asian (EAS) AF: 0.130 AC: 672 AN: 5184

South Asian (SAS) AF: 0.136 AC: 654 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1676 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12061 AN: 68000

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.159 Hom.: 572

Bravo AF: 0.146

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.12
DANN	Benign	0.22
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7124828; hg19: chr11-93299743;