rs1002658

Variant names:

• chr6-137660447-C-T
• rs1002658
• ENST00000642830.1:n.39-1709C>T

Variant summary

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

The ENST00000642830.1(LINC03004):​n.39-1709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,118 control chromosomes in the GnomAD database, including 1,842 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 (1842 hom., cov: 33)
• Consequence: LINC03004 ENST00000642830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 15 publications found

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642830.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000642830.1		n.39-1709C>T		intron	N/A
	LINC03004	ENST00000691587.2		n.219+2412C>T		intron	N/A
	LINC03004	ENST00000692965.3		n.62-1709C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22527 AN: 152000 Hom.: 1845 Cov.: 33

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.148 AC: 22512 AN: 152118 Hom.: 1842 Cov.: 33 AF XY: 0.146 AC XY: 10889 AN XY: 74344

African (AFR) AF: 0.0760 AC: 3157 AN: 41524

American (AMR) AF: 0.181 AC: 2767 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.0946 AC: 490 AN: 5182

South Asian (SAS) AF: 0.185 AC: 892 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1486 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12393 AN: 67964

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.173 Hom.: 2067

Bravo AF: 0.150

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1002658; hg19: chr6-137981584;