ENST00000642830.1:n.39-1765T>C

Variant names:

• chr6-137660391-T-C
• rs489738
• ENST00000642830.1:n.39-1765T>C

Variant summary

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

The ENST00000642830.1(LINC03004):​n.39-1765T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,126 control chromosomes in the GnomAD database, including 5,848 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 0.27 (5848 hom., cov: 33)
• Consequence: LINC03004 ENST00000642830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 6 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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.39-1765T>C		intron	N/A
	LINC03004	ENST00000691587.2		n.219+2356T>C		intron	N/A
	LINC03004	ENST00000692965.3		n.62-1765T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40952 AN: 152006 Hom.: 5830 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.270 AC: 41011 AN: 152126 Hom.: 5848 Cov.: 33 AF XY: 0.265 AC XY: 19737 AN XY: 74382

African (AFR) AF: 0.361 AC: 14980 AN: 41486

American (AMR) AF: 0.204 AC: 3115 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1860 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1193 AN: 4822

European-Finnish (FIN) AF: 0.206 AC: 2184 AN: 10596

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15996 AN: 67974

Other (OTH) AF: 0.244 AC: 516 AN: 2116

Alfa AF: 0.245 Hom.: 1050

Bravo AF: 0.271

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs489738; hg19: chr6-137981528;