chr2-64799195-T-A

Variant names:

• chr2-64799195-T-A
• rs888351
• ENST00000772000.1:n.441+14453A>T

Variant summary

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

The ENST00000772000.1(LINC01800):​n.441+14453A>T 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 152,238 control chromosomes in the GnomAD database, including 65,318 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 (65318 hom., cov: 31)
• Consequence: LINC01800 ENST00000772000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• 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=-0.67).
• 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+14453A>T		intron	N/A
	LINC01800	ENST00000772002.1		n.322+14453A>T		intron	N/A
	LINC01800	ENST00000772003.1		n.210+14502A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140826 AN: 152120 Hom.: 65266 Cov.: 31

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.926 AC: 140937 AN: 152238 Hom.: 65318 Cov.: 31 AF XY: 0.924 AC XY: 68768 AN XY: 74414

African (AFR) AF: 0.961 AC: 39922 AN: 41546

American (AMR) AF: 0.945 AC: 14452 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3470

East Asian (EAS) AF: 0.914 AC: 4738 AN: 5186

South Asian (SAS) AF: 0.970 AC: 4686 AN: 4832

European-Finnish (FIN) AF: 0.850 AC: 8987 AN: 10568

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

European-Non Finnish (NFE) AF: 0.908 AC: 61785 AN: 68022

Other (OTH) AF: 0.939 AC: 1984 AN: 2112

Alfa AF: 0.902 Hom.: 3391

Bravo AF: 0.933

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	-0.67
CADD	Benign	3.7
DANN	Benign	0.87
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs888351; hg19: chr2-65026329;