15-97041640-C-T

Variant names:

• chr15-97041640-C-T
• rs12442098
• ENST00000740177.1:n.296-49383C>T

Variant summary

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

The ENST00000740177.1(LINC02253):​n.296-49383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 151,502 control chromosomes in the GnomAD database, including 756 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 0.084 (756 hom., cov: 32)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 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.296-49383C>T		intron_variant	Intron 1 of 6
LINC02253	ENST00000740178.1	n.237-49383C>T		intron_variant	Intron 1 of 5
LINC02253	ENST00000740179.1	n.203-49383C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12712 AN: 151392 Hom.: 752 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0840 AC: 12724 AN: 151502 Hom.: 756 Cov.: 32 AF XY: 0.0867 AC XY: 6415 AN XY: 74026

African (AFR) AF: 0.0229 AC: 949 AN: 41406

American (AMR) AF: 0.174 AC: 2634 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 313 AN: 3458

East Asian (EAS) AF: 0.0959 AC: 495 AN: 5160

South Asian (SAS) AF: 0.123 AC: 593 AN: 4814

European-Finnish (FIN) AF: 0.0954 AC: 991 AN: 10384

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0949 AC: 6437 AN: 67800

Other (OTH) AF: 0.0870 AC: 183 AN: 2104

Alfa AF: 0.0941 Hom.: 348

Bravo AF: 0.0859

Asia WGS AF: 0.121 AC: 416 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12442098; hg19: chr15-97584870;