rs276865

Variant names:

• chr15-39264234-G-A
• rs276865
• ENST00000558209.1:n.451+95555C>T

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+95555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,692 control chromosomes in the GnomAD database, including 26,564 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 0.54 (26564 hom., cov: 30)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 1 publications found

Genes affected

ENSG00000259345 (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 (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+156310C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000558209.1	n.451+95555C>T		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000560484.1	n.67+156675C>T		intron_variant	Intron 1 of 3	4
ENSG00000259345	ENST00000561058.5	n.44+9606C>T		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82531 AN: 151574 Hom.: 26494 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.545 AC: 82664 AN: 151692 Hom.: 26564 Cov.: 30 AF XY: 0.543 AC XY: 40259 AN XY: 74112

African (AFR) AF: 0.878 AC: 36341 AN: 41414

American (AMR) AF: 0.556 AC: 8449 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3464

East Asian (EAS) AF: 0.800 AC: 4101 AN: 5124

South Asian (SAS) AF: 0.581 AC: 2788 AN: 4802

European-Finnish (FIN) AF: 0.278 AC: 2924 AN: 10518

Middle Eastern (MID) AF: 0.417 AC: 121 AN: 290

European-Non Finnish (NFE) AF: 0.372 AC: 25257 AN: 67862

Other (OTH) AF: 0.510 AC: 1079 AN: 2114

Alfa AF: 0.460 Hom.: 31867

Bravo AF: 0.578

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.30
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs276865; hg19: chr15-39556435;