11-79982244-A-T

Variant names:

• chr11-79982244-A-T
• rs694575

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 0.551 in 150,888 control chromosomes in the GnomAD database, including 23,392 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 0.55 (23392 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.551 AC: 83085 AN: 150770 Hom.: 23339 Cov.: 30

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.551 AC: 83199 AN: 150888 Hom.: 23392 Cov.: 30 AF XY: 0.562 AC XY: 41407 AN XY: 73642

African (AFR) AF: 0.586 AC: 24094 AN: 41122

American (AMR) AF: 0.589 AC: 8916 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1671 AN: 3456

East Asian (EAS) AF: 0.854 AC: 4361 AN: 5108

South Asian (SAS) AF: 0.577 AC: 2747 AN: 4760

European-Finnish (FIN) AF: 0.639 AC: 6633 AN: 10386

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.491 AC: 33235 AN: 67620

Other (OTH) AF: 0.525 AC: 1102 AN: 2100

Alfa AF: 0.530 Hom.: 2702

Bravo AF: 0.551

Asia WGS AF: 0.702 AC: 2439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.43
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs694575; hg19: chr11-79693287; COSMIC: COSV57767149;