6-137672095-A-G

Variant names:

• chr6-137672095-A-G
• rs675520
• ENST00000642830.1:n.501A>G

Variant summary

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

The ENST00000642830.1(LINC03004):​n.501A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,902 control chromosomes in the GnomAD database, including 21,422 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 0.53 (21422 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC03004 ENST00000642830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 14 publications found

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

LOC105378018 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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
	LINC03004	NR_125867.1		n.170A>G		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000642830.1		n.501A>G		non_coding_transcript_exon	Exon 5 of 7
	LINC03004	ENST00000691587.2		n.389A>G		non_coding_transcript_exon	Exon 3 of 5
	LINC03004	ENST00000692965.3		n.364A>G		non_coding_transcript_exon	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80592 AN: 151784 Hom.: 21398 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.516

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.531 AC: 80653 AN: 151902 Hom.: 21422 Cov.: 32 AF XY: 0.525 AC XY: 39006 AN XY: 74230

African (AFR) AF: 0.584 AC: 24207 AN: 41458

American (AMR) AF: 0.513 AC: 7822 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2041 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2374 AN: 5182

South Asian (SAS) AF: 0.490 AC: 2358 AN: 4812

European-Finnish (FIN) AF: 0.448 AC: 4715 AN: 10524

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35295 AN: 67892

Other (OTH) AF: 0.511 AC: 1075 AN: 2104

Alfa AF: 0.516 Hom.: 4147

Bravo AF: 0.540

Asia WGS AF: 0.431 AC: 1493 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.64
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs675520; hg19: chr6-137993232;