chr2-125714032-C-G

Variant names:

• chr2-125714032-C-G
• rs7603130
• ENST00000430692.1:n.402+2662C>G

Variant summary

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

The ENST00000651223.2(ENSG00000286206):​n.405-2854C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,968 control chromosomes in the GnomAD database, including 24,032 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 0.55 (24032 hom., cov: 32)
• Consequence: ENSG00000286206 ENST00000651223.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 publications found

Genes affected

ENSG00000286206 (HGNC:):

LINC01889 (HGNC:52708): (long intergenic non-protein coding RNA 1889)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651223.2. 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
	ENSG00000286206	ENST00000430692.1	TSL:5	n.402+2662C>G		intron	N/A
	ENSG00000286206	ENST00000651223.2		n.405-2854C>G		intron	N/A
	ENSG00000286206	ENST00000716118.1		n.468+2662C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84278 AN: 151850 Hom.: 24016 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.555 AC: 84313 AN: 151968 Hom.: 24032 Cov.: 32 AF XY: 0.554 AC XY: 41154 AN XY: 74292

African (AFR) AF: 0.441 AC: 18274 AN: 41426

American (AMR) AF: 0.628 AC: 9608 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3834 AN: 5146

South Asian (SAS) AF: 0.723 AC: 3489 AN: 4824

European-Finnish (FIN) AF: 0.476 AC: 5022 AN: 10556

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40525 AN: 67946

Other (OTH) AF: 0.537 AC: 1131 AN: 2108

Alfa AF: 0.422 Hom.: 1092

Bravo AF: 0.561

Asia WGS AF: 0.732 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.048
DANN	Benign	0.42
PhyloP100		-1.3

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: rs7603130;

hg19: chr2-126471609;