2-64799326-A-G

Variant names:

• chr2-64799326-A-G
• rs2098480
• ENST00000772000.1:n.441+14322T>C

Variant summary

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

The ENST00000772000.1(LINC01800):​n.441+14322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 151,844 control chromosomes in the GnomAD database, including 65,235 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 0.93 (65235 hom., cov: 27)
• Consequence: LINC01800 ENST00000772000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

LINC01800 (HGNC:52590): (long intergenic non-protein coding RNA 1800)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772000.1. 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
	LINC01800	ENST00000772000.1		n.441+14322T>C		intron	N/A
	LINC01800	ENST00000772002.1		n.322+14322T>C		intron	N/A
	LINC01800	ENST00000772003.1		n.210+14371T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140554 AN: 151726 Hom.: 65182 Cov.: 27

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.926 AC: 140666 AN: 151844 Hom.: 65235 Cov.: 27 AF XY: 0.925 AC XY: 68580 AN XY: 74164

African (AFR) AF: 0.961 AC: 39797 AN: 41402

American (AMR) AF: 0.946 AC: 14434 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.914 AC: 4711 AN: 5154

South Asian (SAS) AF: 0.970 AC: 4664 AN: 4810

European-Finnish (FIN) AF: 0.849 AC: 8893 AN: 10474

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61771 AN: 67964

Other (OTH) AF: 0.939 AC: 1975 AN: 2104

Alfa AF: 0.921 Hom.: 8343

Bravo AF: 0.934

Asia WGS AF: 0.949 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.44
PhyloP100		-1.0

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: rs2098480;

hg19: chr2-65026460;