15-60260035-G-C

Variant names:

• chr15-60260035-G-C
• rs10519009

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 0.195 in 152,144 control chromosomes in the GnomAD database, including 3,400 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 0.20 (3400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.195 AC: 29645 AN: 152026 Hom.: 3389 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.195 AC: 29694 AN: 152144 Hom.: 3400 Cov.: 32 AF XY: 0.190 AC XY: 14122 AN XY: 74378

African (AFR) AF: 0.322 AC: 13365 AN: 41488

American (AMR) AF: 0.115 AC: 1766 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.116 AC: 598 AN: 5174

South Asian (SAS) AF: 0.0948 AC: 456 AN: 4808

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10592

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10939 AN: 67996

Other (OTH) AF: 0.175 AC: 371 AN: 2114

Alfa AF: 0.176 Hom.: 331

Bravo AF: 0.198

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10519009; hg19: chr15-60552234;