11-34478532-A-G

Variant names:

• chr11-34478532-A-G
• rs1535721

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 0.652 in 152,056 control chromosomes in the GnomAD database, including 35,075 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 0.65 (35075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99155 AN: 151938 Hom.: 35070 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.571

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.652 AC: 99187 AN: 152056 Hom.: 35075 Cov.: 31 AF XY: 0.656 AC XY: 48752 AN XY: 74324

African (AFR) AF: 0.369 AC: 15280 AN: 41452

American (AMR) AF: 0.697 AC: 10645 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2331 AN: 5168

South Asian (SAS) AF: 0.807 AC: 3889 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8382 AN: 10566

Middle Eastern (MID) AF: 0.593 AC: 172 AN: 290

European-Non Finnish (NFE) AF: 0.792 AC: 53837 AN: 67988

Other (OTH) AF: 0.660 AC: 1392 AN: 2110

Alfa AF: 0.753 Hom.: 74046

Bravo AF: 0.629

Asia WGS AF: 0.613 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs1535721; hg19: chr11-34500079;