rs1993976

Positions:

• chr15-98063084-G-A

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.314-16345C>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 0.447 in 151,846 control chromosomes in the GnomAD database, including 15,295 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 (15295 hom., cov: 32)
• Consequence: ENST00000560360.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

(HGNC:):

LINC02251 (HGNC:53149): (long intergenic non-protein coding RNA 2251)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560360.2	n.314-16345C>T		intron_variant, non_coding_transcript_variant		5
LINC02251	ENST00000649950.1	n.393-24054G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67803 AN: 151728 Hom.: 15282 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.447 AC: 67853 AN: 151846 Hom.: 15295 Cov.: 32 AF XY: 0.448 AC XY: 33258 AN XY: 74234

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.430

Alfa AF: 0.438 Hom.: 6919

Bravo AF: 0.443

Asia WGS AF: 0.412 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993976; hg19: chr15-98606313;