rs2623047

Variant names:

• chr8-69466261-A-G
• rs2623047
• ENST00000720959.1:n.92+29570T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-69466261-A-G
• chr8-69466261-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000720959.1(LINC01603):​n.92+29570T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,998 control chromosomes in the GnomAD database, including 17,906 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 0.47 (17906 hom., cov: 32)
• Consequence: LINC01603 ENST00000720959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16
• Publications: 10 publications found

Genes affected

LINC01603 (HGNC:51652): (long intergenic non-protein coding RNA 1603)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720959.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01603	ENST00000720959.1		n.92+29570T>C		intron	N/A
	LINC01603	ENST00000720960.1		n.506+25431T>C		intron	N/A
	LINC01603	ENST00000720961.1		n.171+25431T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71774 AN: 151880 Hom.: 17865 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.473 AC: 71867 AN: 151998 Hom.: 17906 Cov.: 32 AF XY: 0.472 AC XY: 35070 AN XY: 74286

African (AFR) AF: 0.624 AC: 25863 AN: 41438

American (AMR) AF: 0.438 AC: 6689 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3271 AN: 5154

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4812

European-Finnish (FIN) AF: 0.396 AC: 4180 AN: 10558

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27246 AN: 67968

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.428 Hom.: 18862

Bravo AF: 0.492

Asia WGS AF: 0.521 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		3.2
PromoterAI		0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2623047; hg19: chr8-70378496;