6-137679978-G-A

Variant names:

• chr6-137679978-G-A
• rs6921233
• ENST00000635999.1:n.433+5854G>A

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+5854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,008 control chromosomes in the GnomAD database, including 18,384 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 0.49 (18384 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635999.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000635999.1	TSL:5	n.433+5854G>A		intron	N/A
	LINC03004	ENST00000638039.2	TSL:5	n.438+5854G>A		intron	N/A
	LINC03004	ENST00000646621.1		n.414+5854G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74588 AN: 151890 Hom.: 18382 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.491 AC: 74609 AN: 152008 Hom.: 18384 Cov.: 32 AF XY: 0.494 AC XY: 36676 AN XY: 74278

African (AFR) AF: 0.535 AC: 22160 AN: 41444

American (AMR) AF: 0.452 AC: 6914 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2776 AN: 5176

South Asian (SAS) AF: 0.447 AC: 2155 AN: 4824

European-Finnish (FIN) AF: 0.547 AC: 5759 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32003 AN: 67966

Other (OTH) AF: 0.498 AC: 1049 AN: 2108

Alfa AF: 0.473 Hom.: 21840

Bravo AF: 0.485

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.55
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs6921233; hg19: chr6-138001115;