1-87222711-A-G

Variant names:

• chr1-87222711-A-G
• rs10873824
• ENST00000640491.1:n.298+2367A>G

Variant summary

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

The ENST00000640491.1(LINC02801):​n.298+2367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,114 control chromosomes in the GnomAD database, including 48,440 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 0.79 (48440 hom., cov: 32)
• Consequence: LINC02801 ENST00000640491.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 4 publications found

Genes affected

LINC02801 (HGNC:54325): (long intergenic non-protein coding RNA 2801)

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 (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640491.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02801	NR_167752.1		n.298+2367A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02801	ENST00000640491.1	TSL:1	n.298+2367A>G		intron	N/A
	LINC02801	ENST00000640362.1	TSL:5	n.330+2367A>G		intron	N/A
	LINC02801	ENST00000640794.1	TSL:5	n.52+1563A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120236 AN: 151996 Hom.: 48392 Cov.: 32

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.791 AC: 120334 AN: 152114 Hom.: 48440 Cov.: 32 AF XY: 0.789 AC XY: 58630 AN XY: 74346

African (AFR) AF: 0.946 AC: 39305 AN: 41554

American (AMR) AF: 0.763 AC: 11653 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2852 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3009 AN: 5162

South Asian (SAS) AF: 0.773 AC: 3725 AN: 4820

European-Finnish (FIN) AF: 0.675 AC: 7118 AN: 10552

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49968 AN: 67956

Other (OTH) AF: 0.803 AC: 1697 AN: 2114

Alfa AF: 0.759 Hom.: 81954

Bravo AF: 0.801

Asia WGS AF: 0.705 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10873824; hg19: chr1-87688394;