chr11-93076039-G-T

Variant names:

• chr11-93076039-G-T
• rs1876602

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 0.424 in 150,788 control chromosomes in the GnomAD database, including 14,417 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 0.42 (14417 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.424 AC: 63849 AN: 150662 Hom.: 14412 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.424 AC: 63879 AN: 150788 Hom.: 14417 Cov.: 33 AF XY: 0.430 AC XY: 31699 AN XY: 73700

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.424

Alfa AF: 0.425 Hom.: 6933

Bravo AF: 0.413

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876602; hg19: chr11-92809205;