chr15-38951256-A-G

Position:

• chr15-38951256-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560484.1(ENSG00000259345):​n.254+22899T>C variant causes a intron, non coding transcript 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: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_007064586.1	n.1527-8972T>C		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064587.1	n.1526+22899T>C		intron_variant, non_coding_transcript_variant
LOC105370777	XR_007064588.1	n.704+22899T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.254+22899T>C		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1	n.158+128197A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.414

Alfa AF: 0.367 Hom.: 9452

Bravo AF: 0.408

Asia WGS AF: 0.455 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1433895; hg19: chr15-39243457;