11-102844950-T-G

Variant names:

• chr11-102844950-T-G
• rs632478

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 0.571 in 152,100 control chromosomes in the GnomAD database, including 25,292 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 0.57 (25292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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: 0.571 AC: 86751 AN: 151982 Hom.: 25253 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.571 AC: 86846 AN: 152100 Hom.: 25292 Cov.: 33 AF XY: 0.580 AC XY: 43098 AN XY: 74334

African (AFR) AF: 0.637 AC: 26459 AN: 41508

American (AMR) AF: 0.636 AC: 9710 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2133 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3481 AN: 5166

South Asian (SAS) AF: 0.698 AC: 3366 AN: 4820

European-Finnish (FIN) AF: 0.607 AC: 6406 AN: 10560

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33420 AN: 67990

Other (OTH) AF: 0.555 AC: 1174 AN: 2114

Alfa AF: 0.535 Hom.: 3264

Bravo AF: 0.576

Asia WGS AF: 0.666 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.56
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs632478; hg19: chr11-102715681;