11-4094034-T-C

Variant names:

• chr11-4094034-T-C
• rs1662162

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 0.784 in 151,994 control chromosomes in the GnomAD database, including 49,367 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 0.78 (49367 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.784 AC: 119104 AN: 151876 Hom.: 49375 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.784 AC: 119130 AN: 151994 Hom.: 49367 Cov.: 31 AF XY: 0.784 AC XY: 58275 AN XY: 74324

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.800

Alfa AF: 0.891 Hom.: 56486

Bravo AF: 0.759

Asia WGS AF: 0.770 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1662162; hg19: chr11-4115264;