14-38872641-C-A

Position:

• chr14-38872641-C-A

Variant summary

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

The NR_039982.1(LINC00639):​n.159+18100G>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 0.144 in 152,142 control chromosomes in the GnomAD database, including 1,901 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 (1901 hom., cov: 33)
• Consequence: LINC00639 NR_039982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00639	NR_039982.1	n.159+18100G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00639	ENST00000658492.1	n.67-33437G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21873 AN: 152024 Hom.: 1894 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.144 AC: 21910 AN: 152142 Hom.: 1901 Cov.: 33 AF XY: 0.148 AC XY: 10978 AN XY: 74396

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0646

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.182

Alfa AF: 0.114 Hom.: 730

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483546; hg19: chr14-39341845;