rs2069311

Variant names:

• chr6-137660090-C-A
• rs2069311
• ENST00000642830.1:n.38+2055C>A

Variant summary

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

The ENST00000642830.1(LINC03004):​n.38+2055C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03004	ENST00000642830.1		n.38+2055C>A		intron	N/A
	LINC03004	ENST00000691587.2		n.219+2055C>A		intron	N/A
	LINC03004	ENST00000692965.3		n.61+2055C>A		intron	N/A

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

African (AFR) AF: 0.126 AC: 5223 AN: 41476

American (AMR) AF: 0.0508 AC: 777 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1058 AN: 5166

South Asian (SAS) AF: 0.0933 AC: 449 AN: 4814

European-Finnish (FIN) AF: 0.0441 AC: 467 AN: 10600

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0359 AC: 2440 AN: 68014

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0559 Hom.: 600

Bravo AF: 0.0718

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2069311; hg19: chr6-137981227;