3-109679724-G-C

Variant names:

• chr3-109679724-G-C
• rs1406493
• ENST00000485384.1:n.29+31589G>C

Variant summary

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

The ENST00000485384.1(ENSG00000242029):​n.29+31589G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,164 control chromosomes in the GnomAD database, including 52,212 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 0.82 (52212 hom., cov: 32)
• Consequence: ENSG00000242029 ENST00000485384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 3 publications found

Genes affected

ENSG00000242029 (HGNC:):

LINC01205 (HGNC:49636): (long intergenic non-protein coding RNA 1205)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485384.1. 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
	ENSG00000242029	ENST00000485384.1	TSL:2	n.29+31589G>C		intron	N/A
	LINC01205	ENST00000658412.1		n.452-430G>C		intron	N/A
	LINC01205	ENST00000659474.1		n.403-430G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125262 AN: 152046 Hom.: 52184 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.824 AC: 125340 AN: 152164 Hom.: 52212 Cov.: 32 AF XY: 0.818 AC XY: 60860 AN XY: 74372

African (AFR) AF: 0.872 AC: 36227 AN: 41538

American (AMR) AF: 0.746 AC: 11388 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2871 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2150 AN: 5164

South Asian (SAS) AF: 0.774 AC: 3728 AN: 4816

European-Finnish (FIN) AF: 0.839 AC: 8900 AN: 10602

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57322 AN: 67996

Other (OTH) AF: 0.798 AC: 1683 AN: 2110

Alfa AF: 0.810 Hom.: 2527

Bravo AF: 0.817

Asia WGS AF: 0.606 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.49
PhyloP100		-2.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1406493;

hg19: chr3-109398571;