11-102547633-C-T

Variant names:

• chr11-102547633-C-T
• rs11225314

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 0.138 in 151,888 control chromosomes in the GnomAD database, including 1,912 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 0.14 (1912 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 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: 0.138 AC: 20919 AN: 151770 Hom.: 1912 Cov.: 31

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.138 AC: 20916 AN: 151888 Hom.: 1912 Cov.: 31 AF XY: 0.144 AC XY: 10688 AN XY: 74198

African (AFR) AF: 0.0356 AC: 1477 AN: 41448

American (AMR) AF: 0.185 AC: 2830 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1473 AN: 5156

South Asian (SAS) AF: 0.147 AC: 707 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2724 AN: 10486

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10938 AN: 67946

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.139 Hom.: 996

Bravo AF: 0.128

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.85
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11225314; hg19: chr11-102418364;