rs6904167

Variant names:

• chr6-137666771-G-A
• rs6904167
• ENST00000642830.1:n.408G>A

Variant summary

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

The ENST00000642830.1(LINC03004):​n.408G>A 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 0.537 in 152,078 control chromosomes in the GnomAD database, including 21,913 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 0.54 (21894 hom., cov: 32)
  • Exomes 𝑓: 0.54 (19 hom.)
• Consequence: LINC03004 ENST00000642830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05
• 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=-0.89).
• 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.94+1032G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000642830.1		n.408G>A		non_coding_transcript_exon	Exon 4 of 7
	LINC03004	ENST00000746621.1		n.284G>A		non_coding_transcript_exon	Exon 3 of 6
	LINC03004	ENST00000746622.1		n.275G>A		non_coding_transcript_exon	Exon 3 of 6

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81480 AN: 151822 Hom.: 21864 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.543 AC: 75 AN: 138 Hom.: 19 Cov.: 0 AF XY: 0.592 AC XY: 45 AN XY: 76

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.543 AC: 75 AN: 138

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: 0.537 AC: 81558 AN: 151940 Hom.: 21894 Cov.: 32 AF XY: 0.532 AC XY: 39506 AN XY: 74240

African (AFR) AF: 0.584 AC: 24198 AN: 41418

American (AMR) AF: 0.564 AC: 8597 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2043 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2426 AN: 5166

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4706 AN: 10524

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

European-Non Finnish (NFE) AF: 0.520 AC: 35355 AN: 67980

Other (OTH) AF: 0.522 AC: 1103 AN: 2114

Alfa AF: 0.524 Hom.: 11687

Bravo AF: 0.548

Asia WGS AF: 0.470 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.31
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs6904167; hg19: chr6-137987908;