11-11226295-T-C

Variant names:

• chr11-11226295-T-C
• rs17347854

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 0.125 in 152,106 control chromosomes in the GnomAD database, including 1,255 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 0.13 (1255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19032 AN: 151988 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.125 AC: 19050 AN: 152106 Hom.: 1255 Cov.: 32 AF XY: 0.125 AC XY: 9265 AN XY: 74344

African (AFR) AF: 0.0929 AC: 3854 AN: 41506

American (AMR) AF: 0.132 AC: 2022 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 546 AN: 3466

East Asian (EAS) AF: 0.0536 AC: 277 AN: 5166

South Asian (SAS) AF: 0.132 AC: 636 AN: 4812

European-Finnish (FIN) AF: 0.0978 AC: 1034 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10180 AN: 67994

Other (OTH) AF: 0.134 AC: 283 AN: 2108

Alfa AF: 0.144 Hom.: 2657

Bravo AF: 0.123

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.81
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs17347854; hg19: chr11-11247842;