chr1-50329935-A-G

Variant names:

• chr1-50329935-A-G
• rs10493150
• ENST00000642061.2:n.113+3570T>C

Variant summary

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

The ENST00000642061.2(LINC02808):​n.113+3570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,142 control chromosomes in the GnomAD database, including 16,021 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 0.45 (16021 hom., cov: 33)
• Consequence: LINC02808 ENST00000642061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 7 publications found

Genes affected

LINC02808 (HGNC:54340): (long intergenic non-protein coding RNA 2808)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642061.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02808	ENST00000642061.2		n.113+3570T>C		intron	N/A
	LINC02808	ENST00000850017.1		n.164+3570T>C		intron	N/A
	LINC02808	ENST00000850025.1		n.166-2304T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68531 AN: 152022 Hom.: 15991 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.451 AC: 68607 AN: 152142 Hom.: 16021 Cov.: 33 AF XY: 0.444 AC XY: 33015 AN XY: 74356

African (AFR) AF: 0.494 AC: 20476 AN: 41486

American (AMR) AF: 0.373 AC: 5699 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3470

East Asian (EAS) AF: 0.132 AC: 684 AN: 5188

South Asian (SAS) AF: 0.407 AC: 1965 AN: 4826

European-Finnish (FIN) AF: 0.394 AC: 4159 AN: 10554

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32162 AN: 68012

Other (OTH) AF: 0.483 AC: 1021 AN: 2116

Alfa AF: 0.447 Hom.: 1986

Bravo AF: 0.451

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.94
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10493150; hg19: chr1-50795607;