15-97170536-G-A

Variant names:

• chr15-97170536-G-A
• rs2045325
• ENST00000740177.1:n.390-65685G>A

Variant summary

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

The ENST00000740177.1(LINC02253):​n.390-65685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,030 control chromosomes in the GnomAD database, including 15,447 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 (15447 hom., cov: 32)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

Genes affected

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 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
LINC02253	ENST00000740177.1	n.390-65685G>A		intron_variant	Intron 2 of 6
LINC02253	ENST00000740178.1	n.331-65685G>A		intron_variant	Intron 2 of 5
LINC02253	ENST00000740179.1	n.297-65685G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67876 AN: 151912 Hom.: 15441 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.447 AC: 67919 AN: 152030 Hom.: 15447 Cov.: 32 AF XY: 0.450 AC XY: 33434 AN XY: 74288

African (AFR) AF: 0.369 AC: 15295 AN: 41482

American (AMR) AF: 0.453 AC: 6920 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1836 AN: 5154

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4826

European-Finnish (FIN) AF: 0.560 AC: 5903 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32793 AN: 67962

Other (OTH) AF: 0.449 AC: 948 AN: 2112

Alfa AF: 0.462 Hom.: 30474

Bravo AF: 0.436

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2045325; hg19: chr15-97713766; COSMIC: COSV56529586;