3-134337039-G-C

Variant names:

• chr3-134337039-G-C
• rs4974491
• ENST00000765780.1:n.205-9725C>G

Variant summary

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

The ENST00000765780.1(ENSG00000299712):​n.205-9725C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,068 control chromosomes in the GnomAD database, including 14,577 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 0.42 (14577 hom., cov: 32)
• Consequence: ENSG00000299712 ENST00000765780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 publications found

Genes affected

ENSG00000299712 (HGNC:):

LINC02004 (HGNC:52838): (long intergenic non-protein coding RNA 2004)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765780.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299712	ENST00000765780.1		n.205-9725C>G		intron	N/A
	ENSG00000299712	ENST00000765781.1		n.70-9725C>G		intron	N/A
	ENSG00000299712	ENST00000765782.1		n.70-10512C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64221 AN: 151948 Hom.: 14561 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.423 AC: 64275 AN: 152068 Hom.: 14577 Cov.: 32 AF XY: 0.432 AC XY: 32131 AN XY: 74336

African (AFR) AF: 0.462 AC: 19143 AN: 41478

American (AMR) AF: 0.488 AC: 7461 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3468

East Asian (EAS) AF: 0.916 AC: 4715 AN: 5146

South Asian (SAS) AF: 0.643 AC: 3090 AN: 4802

European-Finnish (FIN) AF: 0.340 AC: 3599 AN: 10596

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23863 AN: 67968

Other (OTH) AF: 0.417 AC: 882 AN: 2114

Alfa AF: 0.215 Hom.: 422

Bravo AF: 0.433

Asia WGS AF: 0.767 AC: 2669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.86
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4974491; hg19: chr3-134055881;