rs741477

Variant names:

• chr2-64839177-A-G
• rs741477
• ENST00000668450.1:n.587+1606A>G

Variant summary

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

The ENST00000668450.1(ENSG00000287123):​n.587+1606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,266 control chromosomes in the GnomAD database, including 720 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 0.084 (720 hom., cov: 31)
• Consequence: ENSG00000287123 ENST00000668450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 5 publications found

Genes affected

ENSG00000287123 (HGNC:):

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287123	ENST00000668450.1	n.587+1606A>G		intron_variant	Intron 1 of 1
LINC01800	ENST00000772000.1	n.243+24237T>C		intron_variant	Intron 1 of 3
LINC01800	ENST00000772001.1	n.596-25332T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12828 AN: 152148 Hom.: 716 Cov.: 31

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0843 AC: 12839 AN: 152266 Hom.: 720 Cov.: 31 AF XY: 0.0820 AC XY: 6102 AN XY: 74458

African (AFR) AF: 0.0300 AC: 1246 AN: 41558

American (AMR) AF: 0.0725 AC: 1109 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3470

East Asian (EAS) AF: 0.0255 AC: 132 AN: 5184

South Asian (SAS) AF: 0.0544 AC: 262 AN: 4820

European-Finnish (FIN) AF: 0.101 AC: 1073 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8483 AN: 68006

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.106 Hom.: 2856

Bravo AF: 0.0782

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs741477; hg19: chr2-65066311;