chr15-85814970-G-C

Variant names:

• chr15-85814970-G-C
• rs10520601

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 0.164 in 152,022 control chromosomes in the GnomAD database, including 2,342 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 0.16 (2342 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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: 0.164 AC: 24931 AN: 151904 Hom.: 2343 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.164 AC: 24969 AN: 152022 Hom.: 2342 Cov.: 33 AF XY: 0.167 AC XY: 12385 AN XY: 74304

African (AFR) AF: 0.250 AC: 10356 AN: 41410

American (AMR) AF: 0.156 AC: 2386 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5172

South Asian (SAS) AF: 0.156 AC: 753 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10574

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7704 AN: 67986

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.0680 Hom.: 81

Bravo AF: 0.168

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.41
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs10520601; hg19: chr15-86358201;