rs7175415

Variant names:

• chr15-48698392-T-C
• rs7175415

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 0.283 in 151,808 control chromosomes in the GnomAD database, including 7,286 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 0.28 (7286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.283 AC: 42857 AN: 151690 Hom.: 7267 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.283 AC: 42915 AN: 151808 Hom.: 7286 Cov.: 32 AF XY: 0.291 AC XY: 21577 AN XY: 74178

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.261

Alfa AF: 0.201 Hom.: 3899

Bravo AF: 0.300

Asia WGS AF: 0.338 AC: 1174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7175415; hg19: chr15-48990589;