2-64807060-A-C

Variant names:

• chr2-64807060-A-C
• rs737366
• ENST00000772000.1:n.441+6588T>G

Variant summary

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

The ENST00000772000.1(LINC01800):​n.441+6588T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.902 in 150,594 control chromosomes in the GnomAD database, including 61,050 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 0.90 (61050 hom., cov: 28)
• Consequence: LINC01800 ENST00000772000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.942 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+6588T>G		intron	N/A
	LINC01800	ENST00000772002.1		n.322+6588T>G		intron	N/A
	LINC01800	ENST00000772003.1		n.210+6637T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.902 AC: 135727 AN: 150478 Hom.: 61006 Cov.: 28

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.902 AC: 135827 AN: 150594 Hom.: 61050 Cov.: 28 AF XY: 0.901 AC XY: 66225 AN XY: 73526

African (AFR) AF: 0.883 AC: 35878 AN: 40616

American (AMR) AF: 0.936 AC: 14191 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3327 AN: 3462

East Asian (EAS) AF: 0.898 AC: 4540 AN: 5056

South Asian (SAS) AF: 0.966 AC: 4614 AN: 4778

European-Finnish (FIN) AF: 0.846 AC: 8809 AN: 10412

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61479 AN: 67796

Other (OTH) AF: 0.925 AC: 1949 AN: 2108

Alfa AF: 0.916 Hom.: 4349

Bravo AF: 0.902

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.14
PhyloP100		-2.1

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: rs737366;

hg19: chr2-65034194;