14-58909737-T-C

Variant names:

• chr14-58909737-T-C
• rs2295426
• ENST00000553762.2:n.864-526T>C

Variant summary

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

The ENST00000555378.5(LINC01500):​n.458-526T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,134 control chromosomes in the GnomAD database, including 4,956 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 0.24 (4956 hom., cov: 32)
• Consequence: LINC01500 ENST00000555378.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 3 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555378.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	NR_110547.1		n.458-526T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000553762.2	TSL:5	n.864-526T>C		intron	N/A
	LINC01500	ENST00000555378.5	TSL:3	n.458-526T>C		intron	N/A
	LINC01500	ENST00000556026.1	TSL:3	n.167-526T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36354 AN: 152016 Hom.: 4953 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36385 AN: 152134 Hom.: 4956 Cov.: 32 AF XY: 0.242 AC XY: 18020 AN XY: 74364

African (AFR) AF: 0.125 AC: 5175 AN: 41534

American (AMR) AF: 0.224 AC: 3419 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2857 AN: 5158

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4818

European-Finnish (FIN) AF: 0.275 AC: 2912 AN: 10576

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18914 AN: 67988

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.252 Hom.: 3102

Bravo AF: 0.234

Asia WGS AF: 0.410 AC: 1424 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2295426; hg19: chr14-59376455;