11-102517147-A-T

Variant names:

• chr11-102517147-A-T
• rs11225297

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 0.0959 in 152,284 control chromosomes in the GnomAD database, including 866 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 0.096 (866 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 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: 0.0960 AC: 14601 AN: 152166 Hom.: 866 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.0959 AC: 14608 AN: 152284 Hom.: 866 Cov.: 33 AF XY: 0.0957 AC XY: 7128 AN XY: 74454

African (AFR) AF: 0.0232 AC: 963 AN: 41568

American (AMR) AF: 0.140 AC: 2144 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3470

East Asian (EAS) AF: 0.175 AC: 910 AN: 5186

South Asian (SAS) AF: 0.0789 AC: 381 AN: 4828

European-Finnish (FIN) AF: 0.120 AC: 1270 AN: 10606

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8241 AN: 68020

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0535 Hom.: 71

Bravo AF: 0.0956

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs11225297; hg19: chr11-102387878;