rs180040

Variant names:

• chr15-97027933-T-C
• rs180040
• ENST00000740177.1:n.295+43209T>C

Variant summary

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

The ENST00000740177.1(LINC02253):​n.295+43209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,148 control chromosomes in the GnomAD database, including 54,908 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 0.85 (54908 hom., cov: 32)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 7 publications found

Genes affected

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

ENSG00000296623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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.295+43209T>C		intron_variant	Intron 1 of 6
LINC02253	ENST00000740178.1	n.236+43209T>C		intron_variant	Intron 1 of 5
LINC02253	ENST00000740179.1	n.202+43209T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128483 AN: 152030 Hom.: 54848 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.845 AC: 128605 AN: 152148 Hom.: 54908 Cov.: 32 AF XY: 0.841 AC XY: 62535 AN XY: 74374

African (AFR) AF: 0.961 AC: 39924 AN: 41550

American (AMR) AF: 0.860 AC: 13130 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3153 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4580 AN: 5162

South Asian (SAS) AF: 0.813 AC: 3916 AN: 4816

European-Finnish (FIN) AF: 0.698 AC: 7379 AN: 10568

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53715 AN: 67990

Other (OTH) AF: 0.876 AC: 1850 AN: 2112

Alfa AF: 0.819 Hom.: 6691

Bravo AF: 0.864

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
DANN	Benign	0.66
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs180040; hg19: chr15-97571163;