6-137690528-G-T

Variant names:

• chr6-137690528-G-T
• rs602414
• ENST00000635999.1:n.433+16404G>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+16404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,926 control chromosomes in the GnomAD database, including 30,214 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 0.63 (30214 hom., cov: 31)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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+16404G>T		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000646621.1	n.601+1839G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95339 AN: 151808 Hom.: 30204 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.628 AC: 95377 AN: 151926 Hom.: 30214 Cov.: 31 AF XY: 0.627 AC XY: 46568 AN XY: 74224

African (AFR) AF: 0.683 AC: 28293 AN: 41430

American (AMR) AF: 0.563 AC: 8599 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.801 AC: 4140 AN: 5168

South Asian (SAS) AF: 0.539 AC: 2593 AN: 4810

European-Finnish (FIN) AF: 0.650 AC: 6839 AN: 10520

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41217 AN: 67934

Other (OTH) AF: 0.628 AC: 1323 AN: 2106

Alfa AF: 0.606 Hom.: 16388

Bravo AF: 0.623

Asia WGS AF: 0.641 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs602414; hg19: chr6-138011665; COSMIC: COSV60285692;