15-79573610-T-C

Position:

• chr15-79573610-T-C

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 0.202 in 152,250 control chromosomes in the GnomAD database, including 3,251 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 (3251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.202 AC: 30793 AN: 152132 Hom.: 3243 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.202 AC: 30816 AN: 152250 Hom.: 3251 Cov.: 33 AF XY: 0.205 AC XY: 15267 AN XY: 74438

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.204

Alfa AF: 0.194 Hom.: 3023

Bravo AF: 0.204

Asia WGS AF: 0.266 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6495420; hg19: chr15-79865952;