15-96909448-A-G

Variant names:

• chr15-96909448-A-G
• rs7173819
• ENST00000832789.1:n.459+3110A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000832789.1(ENSG00000308250):​n.459+3110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,012 control chromosomes in the GnomAD database, including 2,694 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 0.18 (2694 hom., cov: 32)
• Consequence: ENSG00000308250 ENST00000832789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

Genes affected

ENSG00000308250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832789.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308250	ENST00000832789.1		n.459+3110A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27185 AN: 151892 Hom.: 2685 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.179 AC: 27206 AN: 152012 Hom.: 2694 Cov.: 32 AF XY: 0.187 AC XY: 13866 AN XY: 74318

African (AFR) AF: 0.199 AC: 8254 AN: 41502

American (AMR) AF: 0.204 AC: 3114 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1810 AN: 5182

South Asian (SAS) AF: 0.157 AC: 759 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2952 AN: 10474

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9172 AN: 67966

Other (OTH) AF: 0.145 AC: 306 AN: 2104

Alfa AF: 0.0678 Hom.: 71

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.043
DANN	Benign	0.35
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7173819; hg19: chr15-97452678;