rs2148117

Variant names:

• chr10-26925017-A-G
• rs2148117

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 0.127 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.127 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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0704

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0429

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0624 Hom.: 487

Bravo AF: 0.146

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2148117; hg19: chr10-27213946;