rs7175415

Positions:

• chr15-48698392-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;