15-67906573-C-T

Variant names:

• chr15-67906573-C-T
• rs448720

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 0.439 in 152,088 control chromosomes in the GnomAD database, including 15,319 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 0.44 (15319 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• 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 = 0.738 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: 0.439 AC: 66664 AN: 151968 Hom.: 15300 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.439 AC: 66712 AN: 152088 Hom.: 15319 Cov.: 33 AF XY: 0.445 AC XY: 33093 AN XY: 74312

African (AFR) AF: 0.342 AC: 14204 AN: 41486

American (AMR) AF: 0.474 AC: 7248 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3923 AN: 5178

South Asian (SAS) AF: 0.665 AC: 3204 AN: 4820

European-Finnish (FIN) AF: 0.424 AC: 4475 AN: 10562

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30424 AN: 67974

Other (OTH) AF: 0.446 AC: 941 AN: 2110

Alfa AF: 0.457 Hom.: 35308

Bravo AF: 0.438

Asia WGS AF: 0.669 AC: 2325 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	5.7
DANN	Benign	0.66
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs448720; hg19: chr15-68198911;