15-87816062-T-A

Variant names:

• chr15-87816062-T-A
• rs11073742
• ENST00000816143.1:n.66-9339T>A

Variant summary

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

The ENST00000816143.1(ENSG00000306185):​n.66-9339T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,890 control chromosomes in the GnomAD database, including 9,599 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 0.35 (9599 hom., cov: 31)
• Consequence: ENSG00000306185 ENST00000816143.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 4 publications found

Genes affected

ENSG00000306185 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816143.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306185	ENST00000816143.1		n.66-9339T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52941 AN: 151772 Hom.: 9590 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.349 AC: 52968 AN: 151890 Hom.: 9599 Cov.: 31 AF XY: 0.353 AC XY: 26185 AN XY: 74234

African (AFR) AF: 0.241 AC: 9966 AN: 41426

American (AMR) AF: 0.374 AC: 5703 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2101 AN: 5126

South Asian (SAS) AF: 0.355 AC: 1706 AN: 4808

European-Finnish (FIN) AF: 0.479 AC: 5057 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26185 AN: 67938

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.228 Hom.: 538

Bravo AF: 0.337

Asia WGS AF: 0.382 AC: 1326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.54
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs11073742; hg19: chr15-88359293;