15-60405637-C-T

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 0.674 in 152,118 control chromosomes in the GnomAD database, including 35,472 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 0.67 (35472 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102395 AN: 152000 Hom.: 35445 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.674 AC: 102474 AN: 152118 Hom.: 35472 Cov.: 33 AF XY: 0.682 AC XY: 50694 AN XY: 74374

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.664

Alfa AF: 0.697 Hom.: 47132

Bravo AF: 0.658

Asia WGS AF: 0.855 AC: 2972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4561404; hg19: chr15-60697836;