15-60417705-G-A

Position:

• chr15-60417705-G-A

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 0.505 in 151,974 control chromosomes in the GnomAD database, including 21,857 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 0.51 (21857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76736 AN: 151856 Hom.: 21838 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.505 AC: 76773 AN: 151974 Hom.: 21857 Cov.: 32 AF XY: 0.519 AC XY: 38515 AN XY: 74262

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.490

Alfa AF: 0.553 Hom.: 30943

Bravo AF: 0.480

Asia WGS AF: 0.778 AC: 2702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11071529; hg19: chr15-60709904;