rs694069

Variant names:

• chr6-137692414-A-G
• rs694069
• ENST00000635999.1:n.433+18290A>G

Variant summary

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

The ENST00000646621.1(LINC03004):​n.601+3725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,128 control chromosomes in the GnomAD database, including 33,468 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 0.66 (33468 hom., cov: 33)
• Consequence: LINC03004 ENST00000646621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646621.1. 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	ENST00000635999.1	TSL:5	n.433+18290A>G		intron	N/A
	LINC03004	ENST00000646621.1		n.601+3725A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100017 AN: 152010 Hom.: 33423 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.658 AC: 100111 AN: 152128 Hom.: 33468 Cov.: 33 AF XY: 0.658 AC XY: 48939 AN XY: 74356

African (AFR) AF: 0.767 AC: 31858 AN: 41512

American (AMR) AF: 0.624 AC: 9547 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4164 AN: 5166

South Asian (SAS) AF: 0.540 AC: 2608 AN: 4828

European-Finnish (FIN) AF: 0.650 AC: 6877 AN: 10576

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.608 AC: 41294 AN: 67972

Other (OTH) AF: 0.657 AC: 1388 AN: 2112

Alfa AF: 0.642 Hom.: 6553

Bravo AF: 0.659

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs694069; hg19: chr6-138013551; COSMIC: COSV60285697;