chr15-70258089-G-A

Variant names:

• chr15-70258089-G-A
• rs10518889
• ENST00000819627.1:n.340+2952G>A

Variant summary

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

The ENST00000819627.1(ENSG00000306606):​n.340+2952G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,160 control chromosomes in the GnomAD database, including 7,585 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 0.31 (7585 hom., cov: 32)
• Consequence: ENSG00000306606 ENST00000819627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306606	ENST00000819627.1	n.340+2952G>A		intron_variant	Intron 2 of 3
ENSG00000306606	ENST00000819628.1	n.291+2952G>A		intron_variant	Intron 2 of 2
ENSG00000306606	ENST00000819629.1	n.257-1558G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46916 AN: 152042 Hom.: 7584 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.308 AC: 46926 AN: 152160 Hom.: 7585 Cov.: 32 AF XY: 0.307 AC XY: 22830 AN XY: 74390

African (AFR) AF: 0.261 AC: 10827 AN: 41522

American (AMR) AF: 0.232 AC: 3550 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3468

East Asian (EAS) AF: 0.103 AC: 534 AN: 5178

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4828

European-Finnish (FIN) AF: 0.427 AC: 4512 AN: 10576

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24162 AN: 67978

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.331 Hom.: 37367

Bravo AF: 0.291

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10518889; hg19: chr15-70550428;