11-2191936-C-T

Variant names:

• chr11-2191936-C-T
• rs7111341

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 0.289 in 152,010 control chromosomes in the GnomAD database, including 6,794 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 0.29 (6794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 68 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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: 0.288 AC: 43805 AN: 151892 Hom.: 6767 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.289 AC: 43871 AN: 152010 Hom.: 6794 Cov.: 32 AF XY: 0.282 AC XY: 20925 AN XY: 74306

African (AFR) AF: 0.393 AC: 16274 AN: 41426

American (AMR) AF: 0.211 AC: 3221 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3466

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5174

South Asian (SAS) AF: 0.150 AC: 721 AN: 4808

European-Finnish (FIN) AF: 0.246 AC: 2603 AN: 10578

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18502 AN: 67964

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.266 Hom.: 26221

Bravo AF: 0.290

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7111341; hg19: chr11-2213166;