rs10140345

Variant names:

• chr14-97164530-A-T
• rs10140345
• ENST00000717121.1:n.536+9361A>T

Variant summary

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

The ENST00000717121.1(LINC02304):​n.536+9361A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,018 control chromosomes in the GnomAD database, including 17,360 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 0.47 (17360 hom., cov: 32)
• Consequence: LINC02304 ENST00000717121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 2 publications found

Genes affected

LINC02304 (HGNC:53223): (long intergenic non-protein coding RNA 2304)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717121.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02304	ENST00000717121.1		n.536+9361A>T		intron	N/A
	LINC02304	ENST00000717122.1		n.294-9055A>T		intron	N/A
	LINC02304	ENST00000726315.1		n.409+9361A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71832 AN: 151900 Hom.: 17338 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.473 AC: 71905 AN: 152018 Hom.: 17360 Cov.: 32 AF XY: 0.461 AC XY: 34248 AN XY: 74296

African (AFR) AF: 0.483 AC: 20016 AN: 41464

American (AMR) AF: 0.408 AC: 6234 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1755 AN: 5168

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4818

European-Finnish (FIN) AF: 0.375 AC: 3954 AN: 10550

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34795 AN: 67956

Other (OTH) AF: 0.473 AC: 1000 AN: 2112

Alfa AF: 0.488 Hom.: 2276

Bravo AF: 0.477

Asia WGS AF: 0.391 AC: 1355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs10140345; hg19: chr14-97630867;