15-48698669-A-G

Variant names:

• chr15-48698669-A-G
• rs7174374

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 0.68 in 152,100 control chromosomes in the GnomAD database, including 35,463 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 0.68 (35463 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 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: 0.680 AC: 103367 AN: 151982 Hom.: 35451 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.680 AC: 103427 AN: 152100 Hom.: 35463 Cov.: 33 AF XY: 0.682 AC XY: 50711 AN XY: 74346

African (AFR) AF: 0.752 AC: 31214 AN: 41494

American (AMR) AF: 0.668 AC: 10201 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4089 AN: 5186

South Asian (SAS) AF: 0.734 AC: 3543 AN: 4826

European-Finnish (FIN) AF: 0.653 AC: 6887 AN: 10552

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42883 AN: 67980

Other (OTH) AF: 0.661 AC: 1395 AN: 2110

Alfa AF: 0.651 Hom.: 11247

Bravo AF: 0.687

Asia WGS AF: 0.715 AC: 2484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.72
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs7174374; hg19: chr15-48990866;