15-59102985-A-C

Variant names:

• chr15-59102985-A-C
• rs10851643

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 0.352 in 151,936 control chromosomes in the GnomAD database, including 9,419 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 0.35 (9419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.441 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: 0.352 AC: 53503 AN: 151818 Hom.: 9408 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.352 AC: 53541 AN: 151936 Hom.: 9419 Cov.: 32 AF XY: 0.355 AC XY: 26369 AN XY: 74256

African (AFR) AF: 0.355 AC: 14705 AN: 41430

American (AMR) AF: 0.420 AC: 6423 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3472

East Asian (EAS) AF: 0.456 AC: 2359 AN: 5172

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3728 AN: 10516

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22547 AN: 67944

Other (OTH) AF: 0.363 AC: 763 AN: 2104

Alfa AF: 0.343 Hom.: 28881

Bravo AF: 0.363

Asia WGS AF: 0.381 AC: 1324 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	0.68
DANN	Benign	0.53
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10851643; hg19: chr15-59395184;