11-34563943-A-C

Position:

• chr11-34563943-A-C

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 0.74 in 152,006 control chromosomes in the GnomAD database, including 42,127 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 0.74 (42127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.740 AC: 112441 AN: 151888 Hom.: 42072 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.740 AC: 112556 AN: 152006 Hom.: 42127 Cov.: 31 AF XY: 0.742 AC XY: 55144 AN XY: 74304

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.735

Alfa AF: 0.701 Hom.: 15198

Bravo AF: 0.752

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1453389; hg19: chr11-34585490;