15-74727502-T-C

Variant names:

• chr15-74727502-T-C
• rs7495708

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 0.31 in 151,064 control chromosomes in the GnomAD database, including 9,606 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 0.31 (9606 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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: 0.309 AC: 46661 AN: 150946 Hom.: 9561 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.310 AC: 46782 AN: 151064 Hom.: 9606 Cov.: 31 AF XY: 0.314 AC XY: 23157 AN XY: 73728

African (AFR) AF: 0.540 AC: 22233 AN: 41140

American (AMR) AF: 0.418 AC: 6353 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3462

East Asian (EAS) AF: 0.518 AC: 2647 AN: 5106

South Asian (SAS) AF: 0.354 AC: 1692 AN: 4786

European-Finnish (FIN) AF: 0.150 AC: 1549 AN: 10358

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10513 AN: 67704

Other (OTH) AF: 0.302 AC: 633 AN: 2094

Alfa AF: 0.0772 Hom.: 97

Bravo AF: 0.337

Asia WGS AF: 0.492 AC: 1704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs7495708; hg19: chr15-75019843;