ENST00000740177.1:n.295+20171T>A

Variant names:

• chr15-97004895-T-A
• rs234511
• ENST00000740177.1:n.295+20171T>A

Variant summary

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

The ENST00000740177.1(LINC02253):​n.295+20171T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,190 control chromosomes in the GnomAD database, including 1,084 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 0.078 (1084 hom., cov: 32)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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+20171T>A		intron_variant	Intron 1 of 6
LINC02253	ENST00000740178.1	n.236+20171T>A		intron_variant	Intron 1 of 5
LINC02253	ENST00000740179.1	n.202+20171T>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11822 AN: 152070 Hom.: 1073 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0780 AC: 11870 AN: 152190 Hom.: 1084 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74406

African (AFR) AF: 0.220 AC: 9107 AN: 41480

American (AMR) AF: 0.0621 AC: 950 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.0544 AC: 281 AN: 5166

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4824

European-Finnish (FIN) AF: 0.00254 AC: 27 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0173 AC: 1179 AN: 68014

Other (OTH) AF: 0.0685 AC: 145 AN: 2116

Alfa AF: 0.00323 Hom.: 1

Bravo AF: 0.0897

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs234511; hg19: chr15-97548125;