chr15-60341655-G-A

Position:

• chr15-60341655-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 0.619 in 152,070 control chromosomes in the GnomAD database, including 29,576 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 0.62 (29576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 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: 0.619 AC: 94045 AN: 151952 Hom.: 29557 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.619 AC: 94107 AN: 152070 Hom.: 29576 Cov.: 32 AF XY: 0.621 AC XY: 46170 AN XY: 74334

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.645

Alfa AF: 0.561 Hom.: 2077

Bravo AF: 0.628

Asia WGS AF: 0.647 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7170178; hg19: chr15-60633854;