chr11-108942877-A-G

Variant names:

• chr11-108942877-A-G
• rs7112835

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 0.213 in 151,616 control chromosomes in the GnomAD database, including 3,597 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 (3597 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 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: 0.213 AC: 32209 AN: 151496 Hom.: 3589 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.213 AC: 32249 AN: 151616 Hom.: 3597 Cov.: 31 AF XY: 0.219 AC XY: 16241 AN XY: 74004

African (AFR) AF: 0.188 AC: 7789 AN: 41400

American (AMR) AF: 0.216 AC: 3288 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5164

South Asian (SAS) AF: 0.255 AC: 1223 AN: 4794

European-Finnish (FIN) AF: 0.292 AC: 3015 AN: 10314

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14144 AN: 67938

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.139 Hom.: 310

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7112835; hg19: chr11-108813604;