14-38881362-A-G

Variant names:

• chr14-38881362-A-G
• rs12432214
• ENST00000554732.5:n.221+9379T>C

Variant summary

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

The ENST00000554732.5(LINC00639):​n.221+9379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,228 control chromosomes in the GnomAD database, including 1,939 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 0.15 (1939 hom., cov: 32)
• Consequence: LINC00639 ENST00000554732.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 5 publications found

Genes affected

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

ENSG00000301174 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554732.5. 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
	LINC00639	NR_039982.1		n.159+9379T>C		intron	N/A
	LOC105370457	NR_135256.1		n.13-1234A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00639	ENST00000554732.5	TSL:1	n.221+9379T>C		intron	N/A
	LINC00639	ENST00000553932.5	TSL:2	n.154+9379T>C		intron	N/A
	LINC00639	ENST00000556116.2	TSL:4	n.246-42158T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22201 AN: 152110 Hom.: 1934 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.146 AC: 22243 AN: 152228 Hom.: 1939 Cov.: 32 AF XY: 0.150 AC XY: 11137 AN XY: 74430

African (AFR) AF: 0.141 AC: 5841 AN: 41542

American (AMR) AF: 0.305 AC: 4661 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3466

East Asian (EAS) AF: 0.0644 AC: 334 AN: 5188

South Asian (SAS) AF: 0.148 AC: 712 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1267 AN: 10596

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8215 AN: 68022

Other (OTH) AF: 0.180 AC: 380 AN: 2116

Alfa AF: 0.155 Hom.: 426

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.7
DANN	Benign	0.81
PhyloP100		2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12432214; hg19: chr14-39350566;