15-74727502-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 0.31 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.302

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7495708; hg19: chr15-75019843;