15-60405637-C-T

Variant names:

• chr15-60405637-C-T
• rs4561404

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.520 AC: 21580 AN: 41462

American (AMR) AF: 0.701 AC: 10711 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3472

East Asian (EAS) AF: 0.934 AC: 4848 AN: 5190

South Asian (SAS) AF: 0.829 AC: 3996 AN: 4822

European-Finnish (FIN) AF: 0.793 AC: 8375 AN: 10562

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.709 AC: 48244 AN: 68006

Other (OTH) AF: 0.664 AC: 1404 AN: 2114

Alfa AF: 0.692 Hom.: 58467

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
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs4561404; hg19: chr15-60697836;