15-70290997-T-A

Variant names:

• chr15-70290997-T-A
• rs1912967
• ENST00000819627.1:n.341-602T>A

Variant summary

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

The ENST00000819627.1(ENSG00000306606):​n.341-602T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,132 control chromosomes in the GnomAD database, including 29,960 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 0.61 (29960 hom., cov: 32)
• Consequence: ENSG00000306606 ENST00000819627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 1 publications found

Genes affected

ENSG00000306606 (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 (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819627.1. 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
	ENSG00000306606	ENST00000819627.1		n.341-602T>A		intron	N/A
	ENSG00000306606	ENST00000819628.1		n.292-602T>A		intron	N/A
	ENSG00000306606	ENST00000819629.1		n.525-602T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92543 AN: 152014 Hom.: 29957 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.609 AC: 92576 AN: 152132 Hom.: 29960 Cov.: 32 AF XY: 0.610 AC XY: 45381 AN XY: 74404

African (AFR) AF: 0.394 AC: 16323 AN: 41478

American (AMR) AF: 0.581 AC: 8885 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2544 AN: 5162

South Asian (SAS) AF: 0.553 AC: 2664 AN: 4820

European-Finnish (FIN) AF: 0.804 AC: 8526 AN: 10606

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49447 AN: 67990

Other (OTH) AF: 0.593 AC: 1254 AN: 2114

Alfa AF: 0.667 Hom.: 4388

Bravo AF: 0.582

Asia WGS AF: 0.487 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.61
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1912967; hg19: chr15-70583336;