15-97570321-A-G

Position:

• chr15-97570321-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 0.636 in 151,954 control chromosomes in the GnomAD database, including 31,215 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 0.64 (31215 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97570321A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287321	ENST00000658524.1	n.227-2185A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96511 AN: 151836 Hom.: 31192 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.636 AC: 96580 AN: 151954 Hom.: 31215 Cov.: 32 AF XY: 0.636 AC XY: 47275 AN XY: 74276

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.628

Alfa AF: 0.493 Hom.: 1360

Bravo AF: 0.645

Asia WGS AF: 0.659 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288392; hg19: chr15-98113551;