rs12432214

Positions:

• chr14-38881362-A-G

Variant summary

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

The NR_039982.1(LINC00639):​n.159+9379T>C 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 0.146 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 NR_039982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

Genes affected

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

LOC105370457 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00639	NR_039982.1	n.159+9379T>C		intron_variant, non_coding_transcript_variant
LOC105370457	NR_135256.1	n.13-1234A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00639	ENST00000658492.1	n.67-42158T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.180

Alfa AF: 0.156 Hom.: 420

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12432214; hg19: chr14-39350566;