rs1662162

chr11-4094034-T-Cchr11-4094034-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;