11-80251105-A-T

Variant names:

• chr11-80251105-A-T
• rs11231991

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 0.0432 in 152,250 control chromosomes in the GnomAD database, including 313 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 0.043 (313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.0432 AC: 6569 AN: 152130 Hom.: 313 Cov.: 32

Gnomad AFR AF: 0.00835

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0432 AC: 6571 AN: 152250 Hom.: 313 Cov.: 32 AF XY: 0.0480 AC XY: 3574 AN XY: 74434

African (AFR) AF: 0.00832 AC: 346 AN: 41570

American (AMR) AF: 0.0397 AC: 608 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1380 AN: 5156

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4826

European-Finnish (FIN) AF: 0.0869 AC: 921 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0406 AC: 2763 AN: 68004

Other (OTH) AF: 0.0321 AC: 68 AN: 2116

Alfa AF: 0.0443 Hom.: 24

Bravo AF: 0.0420

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.064
DANN	Benign	0.69
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11231991; hg19: chr11-79962149;