chr15-60407409-C-T

Variant names:

• chr15-60407409-C-T
• rs1545540

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 0.622 in 152,146 control chromosomes in the GnomAD database, including 32,067 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 (32067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.622 AC: 94598 AN: 152028 Hom.: 32053 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.622 AC: 94637 AN: 152146 Hom.: 32067 Cov.: 32 AF XY: 0.632 AC XY: 47005 AN XY: 74394

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.631

Alfa AF: 0.613 Hom.: 2371

Bravo AF: 0.600

Asia WGS AF: 0.842 AC: 2925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545540; hg19: chr15-60699608;