rs6904167

chr6-137666771-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125867.1(LINC03004):n.94+1032G>A variant causes a intron, non coding transcript 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 NR_125867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03004	NR_125867.1	n.94+1032G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000642830.1	n.408G>A		non_coding_transcript_exon_variant	4/7
LINC03004	ENST00000691587.1	n.132+1032G>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000692965.2	n.265+1032G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 EAS exome AF: 0.543

GnomAD4 genome AF: 0.537 AC: 81558 AN: 151940 Hom.: 21894 Cov.: 32 AF XY: 0.532 AC XY: 39506 AN XY: 74240

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.522

Alfa AF: 0.522 Hom.: 9820

Bravo AF: 0.548

Asia WGS AF: 0.470 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6904167; hg19: chr6-137987908;