rs17108400

chr14-38841818-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_039982.1(LINC00639):n.160-2614C>T variant causes a intron, non coding transcript 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 NR_039982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00639	NR_039982.1	n.160-2614C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00639	ENST00000658492.1	n.67-2614C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.175

Alfa AF: 0.151 Hom.: 429

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17108400; hg19: chr14-39311022;