chr3-73874059-A-C

Variant names:

• chr3-73874059-A-C
• rs1441443
• ENST00000498832.1:n.254+4098A>C

Variant summary

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

The ENST00000498832.1(LINC02005):​n.254+4098A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,072 control chromosomes in the GnomAD database, including 8,937 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 0.32 (8937 hom., cov: 32)
• Consequence: LINC02005 ENST00000498832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 6 publications found

Genes affected

LINC02005 (HGNC:52839): (long intergenic non-protein coding RNA 2005)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498832.1. 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
	LINC02005	NR_146637.1		n.348+4098A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02005	ENST00000498832.1	TSL:3	n.254+4098A>C		intron	N/A
	LINC02005	ENST00000659853.1		n.356+4098A>C		intron	N/A
	LINC02005	ENST00000664767.1		n.224+4098A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48596 AN: 151954 Hom.: 8935 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.320 AC: 48635 AN: 152072 Hom.: 8937 Cov.: 32 AF XY: 0.327 AC XY: 24289 AN XY: 74340

African (AFR) AF: 0.420 AC: 17401 AN: 41460

American (AMR) AF: 0.407 AC: 6225 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3871 AN: 5142

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4828

European-Finnish (FIN) AF: 0.259 AC: 2737 AN: 10576

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15359 AN: 67998

Other (OTH) AF: 0.307 AC: 650 AN: 2114

Alfa AF: 0.264 Hom.: 16963

Bravo AF: 0.343

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs1441443; hg19: chr3-73923210;