rs7175415

Variant names:

• chr15-48698392-T-C
• rs7175415

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 0.283 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.420 AC: 17356 AN: 41334

American (AMR) AF: 0.365 AC: 5569 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2490 AN: 5156

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3299 AN: 10498

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11639 AN: 67970

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.218 Hom.: 6675

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
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7175415; hg19: chr15-48990589;