15-79573610-T-C

Variant names:

• chr15-79573610-T-C
• rs6495420

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;