15-25632668-T-G

Variant names:

• chr15-25632668-T-G
• rs2930593

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 0.941 in 152,258 control chromosomes in the GnomAD database, including 67,705 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 0.94 (67705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.971 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: 0.941 AC: 143152 AN: 152140 Hom.: 67663 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.941 AC: 143251 AN: 152258 Hom.: 67705 Cov.: 32 AF XY: 0.943 AC XY: 70187 AN XY: 74434

African (AFR) AF: 0.841 AC: 34951 AN: 41544

American (AMR) AF: 0.976 AC: 14938 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3412 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5018 AN: 5138

South Asian (SAS) AF: 0.995 AC: 4796 AN: 4822

European-Finnish (FIN) AF: 0.985 AC: 10461 AN: 10620

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66462 AN: 68034

Other (OTH) AF: 0.953 AC: 2017 AN: 2116

Alfa AF: 0.966 Hom.: 215980

Bravo AF: 0.937

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.39
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2930593; hg19: chr15-25877815;