11-67265605-C-T

Variant names:

• chr11-67265605-C-T
• rs11605263

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0264 in 152,204 control chromosomes in the GnomAD database, including 80 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 0.026 (80 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0264 (4013/152204) while in subpopulation NFE AF = 0.0438 (2981/67982). AF 95% confidence interval is 0.0425. There are 80 homozygotes in GnomAd4. There are 1817 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 80 gene

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: 0.0264 AC: 4017 AN: 152086 Hom.: 80 Cov.: 31

Gnomad AFR AF: 0.00703

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0264 AC: 4013 AN: 152204 Hom.: 80 Cov.: 31 AF XY: 0.0244 AC XY: 1817 AN XY: 74414

African (AFR) AF: 0.00701 AC: 291 AN: 41528

American (AMR) AF: 0.0189 AC: 289 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4816

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2981 AN: 67982

Other (OTH) AF: 0.0299 AC: 63 AN: 2110

Alfa AF: 0.0395 Hom.: 357

Bravo AF: 0.0270

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs11605263; hg19: chr11-67033076;