rs10851643

chr15-59102985-A-Cchr15-59102985-A-Gchr15-59102985-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.363

Alfa AF: 0.340 Hom.: 18000

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10851643; hg19: chr15-59395184;