chr11-69725959-T-C

Variant names:

• chr11-69725959-T-C
• rs4980684

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 0.527 in 152,068 control chromosomes in the GnomAD database, including 21,931 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 0.53 (21931 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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: 0.527 AC: 80081 AN: 151950 Hom.: 21910 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.527 AC: 80132 AN: 152068 Hom.: 21931 Cov.: 33 AF XY: 0.522 AC XY: 38801 AN XY: 74350

African (AFR) AF: 0.417 AC: 17294 AN: 41450

American (AMR) AF: 0.662 AC: 10120 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4048 AN: 5170

South Asian (SAS) AF: 0.456 AC: 2196 AN: 4818

European-Finnish (FIN) AF: 0.419 AC: 4438 AN: 10588

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37767 AN: 67972

Other (OTH) AF: 0.586 AC: 1238 AN: 2112

Alfa AF: 0.549 Hom.: 18833

Bravo AF: 0.548

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.66
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs4980684; hg19: chr11-69540727;