rs7493138

Variant names:

• chr14-28552722-C-T
• rs7493138
• ENST00000757289.1:n.384+7539G>A

Variant summary

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

The ENST00000757289.1(LINC02300):​n.384+7539G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,832 control chromosomes in the GnomAD database, including 11,027 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 0.38 (11027 hom., cov: 32)
• Consequence: LINC02300 ENST00000757289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 7 publications found

Genes affected

LINC02300 (HGNC:53219): (long intergenic non-protein coding RNA 2300)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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
LINC02300	ENST00000757289.1	n.384+7539G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57054 AN: 151716 Hom.: 11020 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.376 AC: 57081 AN: 151832 Hom.: 11027 Cov.: 32 AF XY: 0.372 AC XY: 27595 AN XY: 74186

African (AFR) AF: 0.337 AC: 13941 AN: 41418

American (AMR) AF: 0.352 AC: 5359 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.124 AC: 640 AN: 5164

South Asian (SAS) AF: 0.271 AC: 1302 AN: 4810

European-Finnish (FIN) AF: 0.398 AC: 4184 AN: 10518

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29063 AN: 67900

Other (OTH) AF: 0.409 AC: 863 AN: 2110

Alfa AF: 0.401 Hom.: 42318

Bravo AF: 0.371

Asia WGS AF: 0.245 AC: 848 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7493138; hg19: chr14-29021928;