6-137678149-C-T

Variant names:

• chr6-137678149-C-T
• rs9376293
• ENST00000635999.1:n.433+4025C>T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+4025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,814 control chromosomes in the GnomAD database, including 29,564 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 0.62 (29564 hom., cov: 30)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 11 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+4025C>T		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2	n.438+4025C>T		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.414+4025C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94294 AN: 151696 Hom.: 29541 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.621 AC: 94350 AN: 151814 Hom.: 29564 Cov.: 30 AF XY: 0.621 AC XY: 46014 AN XY: 74156

African (AFR) AF: 0.695 AC: 28775 AN: 41388

American (AMR) AF: 0.551 AC: 8393 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3785 AN: 5160

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4814

European-Finnish (FIN) AF: 0.634 AC: 6648 AN: 10490

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40435 AN: 67926

Other (OTH) AF: 0.617 AC: 1305 AN: 2116

Alfa AF: 0.548 Hom.: 3427

Bravo AF: 0.617

Asia WGS AF: 0.634 AC: 2202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9376293; hg19: chr6-137999286; COSMIC: COSV71077270;