rs397425

Variant names:

• chr5-28921153-G-A
• rs397425
• ENST00000658190.1:n.818+111005G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-28921153-G-A
• chr5-28921153-G-C

Variant summary

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

The ENST00000658190.1(LINC02109):​n.818+111005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,748 control chromosomes in the GnomAD database, including 16,122 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 0.46 (16122 hom., cov: 32)
• Consequence: LINC02109 ENST00000658190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 9 publications found

Genes affected

LINC02109 (HGNC:52964): (long intergenic non-protein coding RNA 2109)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658190.1. 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
	LINC02109	ENST00000658190.1		n.818+111005G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69295 AN: 151630 Hom.: 16109 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.457 AC: 69339 AN: 151748 Hom.: 16122 Cov.: 32 AF XY: 0.457 AC XY: 33885 AN XY: 74164

African (AFR) AF: 0.430 AC: 17808 AN: 41396

American (AMR) AF: 0.409 AC: 6226 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3462

East Asian (EAS) AF: 0.692 AC: 3566 AN: 5150

South Asian (SAS) AF: 0.604 AC: 2909 AN: 4814

European-Finnish (FIN) AF: 0.434 AC: 4585 AN: 10562

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31042 AN: 67820

Other (OTH) AF: 0.471 AC: 992 AN: 2104

Alfa AF: 0.456 Hom.: 25532

Bravo AF: 0.453

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.53
PhyloP100		-3.1

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: rs397425;

hg19: chr5-28921260;