rs626750

Positions:

• chr11-102850214-G-A
• chr11-102850214-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.205

Alfa AF: 0.114 Hom.: 182

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs626750; hg19: chr11-102720945;