ENST00000554732.5:n.222-2614C>T

Variant names:

• chr14-38841818-G-A
• rs17108400
• ENST00000554732.5:n.222-2614C>T

Variant summary

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

The ENST00000554732.5(LINC00639):​n.222-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,102 control chromosomes in the GnomAD database, including 1,917 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 0.14 (1917 hom., cov: 32)
• Consequence: LINC00639 ENST00000554732.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 4 publications found

Genes affected

LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00639	NR_039982.1	n.160-2614C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00639	ENST00000554732.5	n.222-2614C>T		intron_variant	Intron 3 of 5	1
LINC00639	ENST00000553932.5	n.155-2614C>T		intron_variant	Intron 2 of 6	2
LINC00639	ENST00000556116.2	n.246-2614C>T		intron_variant	Intron 2 of 7	4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21972 AN: 151984 Hom.: 1913 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.145 AC: 22007 AN: 152102 Hom.: 1917 Cov.: 32 AF XY: 0.150 AC XY: 11175 AN XY: 74356

African (AFR) AF: 0.143 AC: 5925 AN: 41488

American (AMR) AF: 0.300 AC: 4589 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3468

East Asian (EAS) AF: 0.102 AC: 528 AN: 5172

South Asian (SAS) AF: 0.162 AC: 782 AN: 4830

European-Finnish (FIN) AF: 0.139 AC: 1465 AN: 10550

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7597 AN: 67988

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.129 Hom.: 2308

Bravo AF: 0.161

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.28
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17108400; hg19: chr14-39311022;