15-51623615-C-T

Variant names:

• chr15-51623615-C-T
• rs10519313

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 0.475 in 152,038 control chromosomes in the GnomAD database, including 17,539 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 0.47 (17539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.475 AC: 72111 AN: 151920 Hom.: 17525 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.475 AC: 72162 AN: 152038 Hom.: 17539 Cov.: 32 AF XY: 0.473 AC XY: 35174 AN XY: 74300

African (AFR) AF: 0.402 AC: 16654 AN: 41466

American (AMR) AF: 0.494 AC: 7555 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1341 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1813 AN: 5166

South Asian (SAS) AF: 0.418 AC: 2011 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5701 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35324 AN: 67976

Other (OTH) AF: 0.468 AC: 988 AN: 2110

Alfa AF: 0.501 Hom.: 2951

Bravo AF: 0.468

Asia WGS AF: 0.382 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10519313; hg19: chr15-51915812;