11-102849947-G-T

Variant names:

• chr11-102849947-G-T
• rs615098

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 0.226 in 152,022 control chromosomes in the GnomAD database, including 4,301 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 0.23 (4301 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 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: 0.226 AC: 34404 AN: 151904 Hom.: 4297 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.226 AC: 34419 AN: 152022 Hom.: 4301 Cov.: 32 AF XY: 0.225 AC XY: 16731 AN XY: 74326

African (AFR) AF: 0.335 AC: 13880 AN: 41462

American (AMR) AF: 0.152 AC: 2311 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3470

East Asian (EAS) AF: 0.135 AC: 699 AN: 5182

South Asian (SAS) AF: 0.175 AC: 843 AN: 4826

European-Finnish (FIN) AF: 0.247 AC: 2616 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12449 AN: 67952

Other (OTH) AF: 0.219 AC: 461 AN: 2108

Alfa AF: 0.195 Hom.: 9658

Bravo AF: 0.224

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.57
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs615098; hg19: chr11-102720678;