chr15-85282336-C-A

Variant names:

• chr15-85282336-C-A
• rs6496932
• ENST00000559518.1:n.152-8168G>T

Variant summary

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

The ENST00000559518.1(ENSG00000291212):​n.152-8168G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,848 control chromosomes in the GnomAD database, including 7,141 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 0.29 (7141 hom., cov: 31)
• Consequence: ENSG00000291212 ENST00000559518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 33 publications found

Genes affected

ENSG00000291212 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559518.1. 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
	ENSG00000291212	ENST00000559518.1	TSL:4	n.152-8168G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43379 AN: 151730 Hom.: 7121 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.286 AC: 43455 AN: 151848 Hom.: 7141 Cov.: 31 AF XY: 0.293 AC XY: 21771 AN XY: 74216

African (AFR) AF: 0.443 AC: 18298 AN: 41350

American (AMR) AF: 0.253 AC: 3860 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1706 AN: 5158

South Asian (SAS) AF: 0.371 AC: 1780 AN: 4802

European-Finnish (FIN) AF: 0.291 AC: 3070 AN: 10536

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12907 AN: 67966

Other (OTH) AF: 0.277 AC: 584 AN: 2108

Alfa AF: 0.222 Hom.: 20047

Bravo AF: 0.286

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6496932; hg19: chr15-85825567;