3-184480655-T-G

Variant names:

• chr3-184480655-T-G
• rs9822959
• ENST00000827608.1:n.173+4583T>G

Variant summary

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

The ENST00000827608.1(ENSG00000307641):​n.173+4583T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,028 control chromosomes in the GnomAD database, including 39,372 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 0.72 (39372 hom., cov: 32)
• Consequence: ENSG00000307641 ENST00000827608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 publications found

Genes affected

ENSG00000307641 (HGNC:):

LINC01839 (HGNC:41330): (long intergenic non-protein coding RNA 1839)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827608.1. 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
	ENSG00000307641	ENST00000827608.1		n.173+4583T>G		intron	N/A
	ENSG00000307641	ENST00000827609.1		n.183+4573T>G		intron	N/A
	ENSG00000307641	ENST00000827610.1		n.165+4583T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108795 AN: 151910 Hom.: 39330 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.716 AC: 108895 AN: 152028 Hom.: 39372 Cov.: 32 AF XY: 0.718 AC XY: 53376 AN XY: 74306

African (AFR) AF: 0.774 AC: 32131 AN: 41496

American (AMR) AF: 0.797 AC: 12166 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2583 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4118 AN: 5168

South Asian (SAS) AF: 0.745 AC: 3586 AN: 4812

European-Finnish (FIN) AF: 0.644 AC: 6791 AN: 10542

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45106 AN: 67958

Other (OTH) AF: 0.744 AC: 1569 AN: 2110

Alfa AF: 0.689 Hom.: 94396

Bravo AF: 0.729

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.24
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9822959; hg19: chr3-184198443; COSMIC: COSV71524929;