15-98081657-A-G

Variant names:

• chr15-98081657-A-G
• rs8027435
• ENST00000560360.2:n.314-34918T>C

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.314-34918T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,816 control chromosomes in the GnomAD database, including 23,544 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 0.55 (23544 hom., cov: 30)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.875

Genes affected

ENSG00000259199 (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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259199	ENST00000560360.2	n.314-34918T>C		intron_variant	Intron 3 of 4	5
LINC02251	ENST00000649950.1	n.393-5481A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83972 AN: 151698 Hom.: 23530 Cov.: 30

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.553 AC: 84022 AN: 151816 Hom.: 23544 Cov.: 30 AF XY: 0.552 AC XY: 40975 AN XY: 74184

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.511

Alfa AF: 0.522 Hom.: 8639

Bravo AF: 0.551

Asia WGS AF: 0.445 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	10
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8027435; hg19: chr15-98624886;