rs8032019

chr15-34699289-A-G

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 0.341 in 151,822 control chromosomes in the GnomAD database, including 8,885 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 0.34 (8885 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.341 AC: 51753 AN: 151704 Hom.: 8875 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.341 AC: 51783 AN: 151822 Hom.: 8885 Cov.: 31 AF XY: 0.339 AC XY: 25177 AN XY: 74222

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.329

Alfa AF: 0.341 Hom.: 1834

Bravo AF: 0.340

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8032019; hg19: chr15-34991490;