chr11-64535478-T-A

Variant names:

• chr11-64535478-T-A
• rs11231809

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 0.31 in 152,086 control chromosomes in the GnomAD database, including 8,551 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 0.31 (8551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47205 AN: 151968 Hom.: 8544 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.310 AC: 47216 AN: 152086 Hom.: 8551 Cov.: 32 AF XY: 0.312 AC XY: 23191 AN XY: 74338

African (AFR) AF: 0.113 AC: 4696 AN: 41504

American (AMR) AF: 0.322 AC: 4928 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5166

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4816

European-Finnish (FIN) AF: 0.418 AC: 4421 AN: 10568

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27506 AN: 67952

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.361 Hom.: 1371

Bravo AF: 0.298

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.63
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11231809; hg19: chr11-64302950;