ENST00000816143.1:n.65+7012T>C

Variant names:

• chr15-87813028-T-C
• rs12913838
• ENST00000816143.1:n.65+7012T>C

Variant summary

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

The ENST00000816143.1(ENSG00000306185):​n.65+7012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,938 control chromosomes in the GnomAD database, including 7,223 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 (7223 hom., cov: 33)
• Consequence: ENSG00000306185 ENST00000816143.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306185	ENST00000816143.1		n.65+7012T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44564 AN: 151822 Hom.: 7225 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.293 AC: 44560 AN: 151938 Hom.: 7223 Cov.: 33 AF XY: 0.295 AC XY: 21894 AN XY: 74238

African (AFR) AF: 0.147 AC: 6081 AN: 41494

American (AMR) AF: 0.374 AC: 5710 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2060 AN: 5140

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4822

European-Finnish (FIN) AF: 0.295 AC: 3103 AN: 10536

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.347 AC: 23581 AN: 67918

Other (OTH) AF: 0.314 AC: 663 AN: 2110

Alfa AF: 0.232 Hom.: 1818

Bravo AF: 0.291

Asia WGS AF: 0.363 AC: 1260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs12913838; hg19: chr15-88356259;