chr15-38902852-G-A

Position:

• chr15-38902852-G-A

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.255-15923C>T 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 0.449 in 152,084 control chromosomes in the GnomAD database, including 15,991 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 0.45 (15991 hom., cov: 33)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.255-15923C>T		intron_variant, non_coding_transcript_variant		4
LINC02694	ENST00000644461.1	n.158+79793G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68233 AN: 151966 Hom.: 15970 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.449 AC: 68299 AN: 152084 Hom.: 15991 Cov.: 33 AF XY: 0.452 AC XY: 33604 AN XY: 74334

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.443

Alfa AF: 0.445 Hom.: 3451

Bravo AF: 0.442

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1821383; hg19: chr15-39195053;