15-70129522-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.323 in 152,128 control chromosomes in the GnomAD database, including 9,306 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 0.32 (9306 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 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: 0.323 AC: 49174 AN: 152010 Hom.: 9297 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.323 AC: 49184 AN: 152128 Hom.: 9306 Cov.: 33 AF XY: 0.330 AC XY: 24537 AN XY: 74370

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.353

Alfa AF: 0.381 Hom.: 10477

Bravo AF: 0.305

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	17
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001597; hg19: chr15-70421861;