rs2069311

Positions:

• chr6-137660090-C-A

Variant summary

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

The ENST00000642830.1(LINC03004):​n.38+2055C>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 0.0703 in 152,156 control chromosomes in the GnomAD database, including 576 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 0.070 (576 hom., cov: 32)
• Consequence: LINC03004 ENST00000642830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000642830.1	n.38+2055C>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000691587.1	n.38+2055C>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000692965.2	n.38+2055C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10689 AN: 152038 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0594

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0703 AC: 10702 AN: 152156 Hom.: 576 Cov.: 32 AF XY: 0.0707 AC XY: 5258 AN XY: 74372

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.0441

Gnomad4 NFE AF: 0.0359

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0540 Hom.: 90

Bravo AF: 0.0718

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069311; hg19: chr6-137981227;