15-23893158-A-G

Variant names:

• chr15-23893158-A-G
• rs10162946

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 0.816 in 151,946 control chromosomes in the GnomAD database, including 51,225 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 0.82 (51225 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.816 AC: 123908 AN: 151828 Hom.: 51204 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.816 AC: 123973 AN: 151946 Hom.: 51225 Cov.: 31 AF XY: 0.817 AC XY: 60667 AN XY: 74262

African (AFR) AF: 0.668 AC: 27638 AN: 41386

American (AMR) AF: 0.881 AC: 13464 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2967 AN: 3468

East Asian (EAS) AF: 0.989 AC: 5066 AN: 5124

South Asian (SAS) AF: 0.856 AC: 4124 AN: 4820

European-Finnish (FIN) AF: 0.811 AC: 8557 AN: 10556

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59276 AN: 68004

Other (OTH) AF: 0.845 AC: 1784 AN: 2110

Alfa AF: 0.856 Hom.: 96752

Bravo AF: 0.817

Asia WGS AF: 0.904 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10162946; hg19: chr15-24138305;