rs10483546

Variant names:

• chr14-38872641-C-A
• rs10483546
• ENST00000554732.5:n.221+18100G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-38872641-C-A
• chr14-38872641-C-G
• chr14-38872641-C-T

Variant summary

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

The ENST00000554732.5(LINC00639):​n.221+18100G>T variant causes a intron 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 ENST00000554732.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 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+18100G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00639	ENST00000554732.5	TSL:1	n.221+18100G>T		intron	N/A
	LINC00639	ENST00000553932.5	TSL:2	n.154+18100G>T		intron	N/A
	LINC00639	ENST00000556116.2	TSL:4	n.246-33437G>T		intron	N/A

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

African (AFR) AF: 0.136 AC: 5622 AN: 41474

American (AMR) AF: 0.304 AC: 4649 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.0646 AC: 335 AN: 5186

South Asian (SAS) AF: 0.151 AC: 728 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10582

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

European-Non Finnish (NFE) AF: 0.119 AC: 8097 AN: 68004

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.122 Hom.: 1172

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.19
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10483546; hg19: chr14-39341845;