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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. 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
	ENSG00000259345	ENST00000558209.1	TSL:3	n.451+95555C>T		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.67+156675C>T		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.44+9606C>T		intron	N/A

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 v4.9

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;