11-2191936-C-T

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 0.289 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.253

Alfa AF: 0.256 Hom.: 11922

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7111341; hg19: chr11-2213166;