rs2148117

Variant names:

• chr10-26925017-A-G
• rs2148117

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 0.127 in 152,050 control chromosomes in the GnomAD database, including 2,547 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 (2547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.127 AC: 19317 AN: 151932 Hom.: 2538 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.127 AC: 19358 AN: 152050 Hom.: 2547 Cov.: 32 AF XY: 0.122 AC XY: 9107 AN XY: 74366

African (AFR) AF: 0.337 AC: 13926 AN: 41354

American (AMR) AF: 0.0902 AC: 1378 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.0704 AC: 365 AN: 5182

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4830

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10612

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0429 AC: 2919 AN: 68006

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.0747 Hom.: 1031

Bravo AF: 0.146

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.020
DANN	Benign	0.22
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2148117; hg19: chr10-27213946;