6-137686393-G-T

Variant names:

• chr6-137686393-G-T
• rs636393
• ENST00000635999.1:n.433+12269G>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+12269G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,926 control chromosomes in the GnomAD database, including 33,243 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 0.66 (33243 hom., cov: 31)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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+12269G>T		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2	n.439-701G>T		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.415-701G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99691 AN: 151808 Hom.: 33207 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.657 AC: 99774 AN: 151926 Hom.: 33243 Cov.: 31 AF XY: 0.657 AC XY: 48767 AN XY: 74260

African (AFR) AF: 0.762 AC: 31604 AN: 41448

American (AMR) AF: 0.624 AC: 9519 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1776 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4156 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4808

European-Finnish (FIN) AF: 0.651 AC: 6873 AN: 10556

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41259 AN: 67910

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.626 Hom.: 64714

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.49
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs636393; hg19: chr6-138007530;