11-34563943-A-C

Variant names:

• chr11-34563943-A-C
• rs1453389

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.781 AC: 32379 AN: 41482

American (AMR) AF: 0.790 AC: 12075 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5108 AN: 5134

South Asian (SAS) AF: 0.848 AC: 4071 AN: 4802

European-Finnish (FIN) AF: 0.653 AC: 6908 AN: 10572

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47182 AN: 67942

Other (OTH) AF: 0.735 AC: 1547 AN: 2104

Alfa AF: 0.706 Hom.: 22509

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1453389; hg19: chr11-34585490;