2-64827805-G-T

Variant names:

• chr2-64827805-G-T
• rs4671615
• ENST00000772000.1:n.244-13960C>A

Variant summary

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

The ENST00000772000.1(LINC01800):​n.244-13960C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,904 control chromosomes in the GnomAD database, including 30,733 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 0.63 (30733 hom., cov: 30)
• Consequence: LINC01800 ENST00000772000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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
LINC01800	ENST00000772000.1	n.244-13960C>A		intron_variant	Intron 1 of 3
LINC01800	ENST00000772001.1	n.596-13960C>A		intron_variant	Intron 1 of 1
LINC01800	ENST00000772002.1	n.124+11202C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95379 AN: 151786 Hom.: 30700 Cov.: 30

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.628 AC: 95466 AN: 151904 Hom.: 30733 Cov.: 30 AF XY: 0.626 AC XY: 46500 AN XY: 74224

African (AFR) AF: 0.760 AC: 31449 AN: 41400

American (AMR) AF: 0.678 AC: 10351 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3468

East Asian (EAS) AF: 0.704 AC: 3647 AN: 5178

South Asian (SAS) AF: 0.558 AC: 2679 AN: 4804

European-Finnish (FIN) AF: 0.500 AC: 5264 AN: 10520

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37670 AN: 67940

Other (OTH) AF: 0.656 AC: 1385 AN: 2110

Alfa AF: 0.580 Hom.: 11301

Bravo AF: 0.647

Asia WGS AF: 0.652 AC: 2267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.66
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4671615; hg19: chr2-65054939;