11-2086624-G-T

Variant names:

• chr11-2086624-G-T
• rs7924489

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 0.761 in 152,068 control chromosomes in the GnomAD database, including 44,281 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 (44281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 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: 0.761 AC: 115597 AN: 151950 Hom.: 44245 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.761 AC: 115689 AN: 152068 Hom.: 44281 Cov.: 32 AF XY: 0.757 AC XY: 56244 AN XY: 74318

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.781

Alfa AF: 0.725 Hom.: 2526

Bravo AF: 0.764

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7924489; hg19: chr11-2107854;