15-38951256-A-G

Variant names:

• chr15-38951256-A-G
• rs1433895
• ENST00000560197.6:n.251+22899T>C

Variant summary

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

The ENST00000560197.6(ENSG00000259345):​n.251+22899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,088 control chromosomes in the GnomAD database, including 12,821 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 0.40 (12821 hom., cov: 33)
• Consequence: ENSG00000259345 ENST00000560197.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 2 publications found

Genes affected

ENSG00000259345 (HGNC:):

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560197.6. 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
	ENSG00000259345	ENST00000560197.6	TSL:5	n.251+22899T>C		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.254+22899T>C		intron	N/A
	ENSG00000259345	ENST00000561058.5	TSL:4	n.311+22899T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61425 AN: 151970 Hom.: 12805 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.404 AC: 61482 AN: 152088 Hom.: 12821 Cov.: 33 AF XY: 0.411 AC XY: 30578 AN XY: 74370

African (AFR) AF: 0.429 AC: 17779 AN: 41466

American (AMR) AF: 0.470 AC: 7176 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3097 AN: 5172

South Asian (SAS) AF: 0.438 AC: 2112 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4618 AN: 10584

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23934 AN: 67980

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.372 Hom.: 13034

Bravo AF: 0.408

Asia WGS AF: 0.455 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1433895; hg19: chr15-39243457;