ENST00000642830.1:n.457G>T

Variant names:

• chr6-137672051-G-T
• rs12206392
• ENST00000642830.1:n.457G>T

Variant summary

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

The ENST00000642830.1(LINC03004):​n.457G>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 ENST00000642830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 2 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=-0.95).
• 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 rank	MANE	Protein	UniProt
LINC03004	NR_125867.1	n.126G>T		non_coding_transcript_exon_variant	Exon 2 of 4
LOC105378018	XR_943058.3	n.386C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000642830.1	n.457G>T		non_coding_transcript_exon_variant	Exon 5 of 7
LINC03004	ENST00000691587.2	n.345G>T		non_coding_transcript_exon_variant	Exon 3 of 5
LINC03004	ENST00000692965.3	n.320G>T		non_coding_transcript_exon_variant	Exon 4 of 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

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

African (AFR) AF: 0.0309 AC: 1282 AN: 41536

American (AMR) AF: 0.0697 AC: 1065 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3468

East Asian (EAS) AF: 0.156 AC: 807 AN: 5186

South Asian (SAS) AF: 0.133 AC: 644 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1088 AN: 10568

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0971 AC: 6595 AN: 67938

Other (OTH) AF: 0.0758 AC: 160 AN: 2110

Alfa AF: 0.0430 Hom.: 41

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12206392; hg19: chr6-137993188;