rs1834459

chr11-35071223-G-Achr11-35071223-G-Cchr11-35071223-G-T

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 0.663 in 151,898 control chromosomes in the GnomAD database, including 34,572 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 0.66 (34572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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: 0.663 AC: 100604 AN: 151778 Hom.: 34525 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.663 AC: 100705 AN: 151898 Hom.: 34572 Cov.: 31 AF XY: 0.666 AC XY: 49447 AN XY: 74208

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.674

Alfa AF: 0.605 Hom.: 3386

Bravo AF: 0.677

Asia WGS AF: 0.774 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.77
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834459; hg19: chr11-35092770;