chr11-102850214-G-A

Variant names:

• chr11-102850214-G-A
• rs626750

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 0.206 in 152,080 control chromosomes in the GnomAD database, including 3,411 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 0.21 (3411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31394 AN: 151962 Hom.: 3408 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.206 AC: 31401 AN: 152080 Hom.: 3411 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74348

African (AFR) AF: 0.268 AC: 11122 AN: 41492

American (AMR) AF: 0.145 AC: 2214 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3468

East Asian (EAS) AF: 0.135 AC: 700 AN: 5192

South Asian (SAS) AF: 0.173 AC: 833 AN: 4824

European-Finnish (FIN) AF: 0.247 AC: 2615 AN: 10582

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12370 AN: 67966

Other (OTH) AF: 0.205 AC: 432 AN: 2106

Alfa AF: 0.180 Hom.: 3474

Bravo AF: 0.201

Asia WGS AF: 0.167 AC: 581 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.32
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs626750; hg19: chr11-102720945;