15-23709102-A-G

Variant names:

• chr15-23709102-A-G
• rs1524842

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 0.456 in 151,748 control chromosomes in the GnomAD database, including 16,240 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 0.46 (16240 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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: 0.456 AC: 69207 AN: 151630 Hom.: 16234 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.456 AC: 69230 AN: 151748 Hom.: 16240 Cov.: 31 AF XY: 0.451 AC XY: 33458 AN XY: 74160

African (AFR) AF: 0.346 AC: 14327 AN: 41360

American (AMR) AF: 0.447 AC: 6818 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3462

East Asian (EAS) AF: 0.363 AC: 1871 AN: 5148

South Asian (SAS) AF: 0.434 AC: 2086 AN: 4804

European-Finnish (FIN) AF: 0.485 AC: 5117 AN: 10544

Middle Eastern (MID) AF: 0.393 AC: 114 AN: 290

European-Non Finnish (NFE) AF: 0.530 AC: 35971 AN: 67890

Other (OTH) AF: 0.456 AC: 961 AN: 2106

Alfa AF: 0.496 Hom.: 14868

Bravo AF: 0.448

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1524842; hg19: chr15-23954249;