chr15-45692873-G-C

Variant names:

• chr15-45692873-G-C
• rs12594515

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 0.435 in 151,938 control chromosomes in the GnomAD database, including 14,815 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 0.43 (14815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.435 AC: 66016 AN: 151820 Hom.: 14802 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66068 AN: 151938 Hom.: 14815 Cov.: 32 AF XY: 0.435 AC XY: 32337 AN XY: 74278

African (AFR) AF: 0.351 AC: 14550 AN: 41446

American (AMR) AF: 0.390 AC: 5947 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2901 AN: 5132

South Asian (SAS) AF: 0.467 AC: 2250 AN: 4814

European-Finnish (FIN) AF: 0.523 AC: 5527 AN: 10566

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32023 AN: 67944

Other (OTH) AF: 0.443 AC: 932 AN: 2106

Alfa AF: 0.451 Hom.: 8215

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.32
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs12594515; hg19: chr15-45985071;