chr15-60405637-C-T

Variant names:

• chr15-60405637-C-T
• rs4561404

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;