11-64543177-C-T

Variant names:

• chr11-64543177-C-T
• rs4930195

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 0.375 in 152,102 control chromosomes in the GnomAD database, including 11,430 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 0.37 (11430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56944 AN: 151984 Hom.: 11431 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.375 AC: 56964 AN: 152102 Hom.: 11430 Cov.: 32 AF XY: 0.369 AC XY: 27445 AN XY: 74356

African (AFR) AF: 0.294 AC: 12211 AN: 41492

American (AMR) AF: 0.305 AC: 4670 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3466

East Asian (EAS) AF: 0.0571 AC: 296 AN: 5182

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4808

European-Finnish (FIN) AF: 0.400 AC: 4236 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31002 AN: 67964

Other (OTH) AF: 0.377 AC: 798 AN: 2114

Alfa AF: 0.430 Hom.: 17274

Bravo AF: 0.364

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.44
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4930195; hg19: chr11-64310649;