rs10520678

Variant names:

• chr15-88394052-C-T
• rs10520678

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 0.355 in 152,108 control chromosomes in the GnomAD database, including 13,140 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 0.36 (13140 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.355 AC: 53963 AN: 151990 Hom.: 13094 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.355 AC: 54060 AN: 152108 Hom.: 13140 Cov.: 33 AF XY: 0.345 AC XY: 25689 AN XY: 74358

African (AFR) AF: 0.700 AC: 29027 AN: 41468

American (AMR) AF: 0.210 AC: 3217 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.111 AC: 574 AN: 5182

South Asian (SAS) AF: 0.311 AC: 1494 AN: 4802

European-Finnish (FIN) AF: 0.173 AC: 1838 AN: 10598

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16149 AN: 67980

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.271 Hom.: 3576

Bravo AF: 0.368

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.59
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10520678; hg19: chr15-88937283;