6-137672051-G-T

Position:

• chr6-137672051-G-T

Variant summary

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

The NR_125867.1(LINC03004):​n.126G>T 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 0.08 in 152,118 control chromosomes in the GnomAD database, including 605 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 0.080 (605 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC03004 NR_125867.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

LINC03004 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03004	NR_125867.1	n.126G>T		non_coding_transcript_exon_variant	2/4
LOC105378018	XR_943058.3	n.386C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000642830.1	n.457G>T		non_coding_transcript_exon_variant	5/7
LINC03004	ENST00000691587.1	n.164G>T		non_coding_transcript_exon_variant	3/5
LINC03004	ENST00000692965.2	n.297G>T		non_coding_transcript_exon_variant	4/6

Frequencies

GnomAD3 genomes AF: 0.0800 AC: 12154 AN: 152000 Hom.: 600 Cov.: 33

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0800 AC: 12169 AN: 152118 Hom.: 605 Cov.: 33 AF XY: 0.0815 AC XY: 6059 AN XY: 74362

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0427 Hom.: 39

Bravo AF: 0.0755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12206392; hg19: chr6-137993188;