4-14142584-A-G

Variant names:

• chr4-14142584-A-G
• rs6844339
• ENST00000715490.1:n.446+80217A>G

Variant summary

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

The ENST00000715490.1(LINC01182):​n.446+80217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 145,320 control chromosomes in the GnomAD database, including 13,173 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 0.41 (13173 hom., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: LINC01182 ENST00000715490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 5 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715490.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	ENST00000715490.1		n.446+80217A>G		intron	N/A
	LINC01182	ENST00000715491.1		n.438-708A>G		intron	N/A
	LINC01182	ENST00000715493.1		n.156+88A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 60228 AN: 145248 Hom.: 13165 Cov.: 24

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.415 AC: 60247 AN: 145320 Hom.: 13173 Cov.: 24 AF XY: 0.410 AC XY: 28845 AN XY: 70268

African (AFR) AF: 0.492 AC: 19239 AN: 39132

American (AMR) AF: 0.342 AC: 5035 AN: 14706

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1444 AN: 3454

East Asian (EAS) AF: 0.128 AC: 645 AN: 5030

South Asian (SAS) AF: 0.420 AC: 1935 AN: 4610

European-Finnish (FIN) AF: 0.347 AC: 2904 AN: 8370

Middle Eastern (MID) AF: 0.451 AC: 129 AN: 286

European-Non Finnish (NFE) AF: 0.414 AC: 27655 AN: 66826

Other (OTH) AF: 0.416 AC: 831 AN: 1996

Alfa AF: 0.359 Hom.: 2278

Bravo AF: 0.418

Asia WGS AF: 0.280 AC: 962 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6844339; hg19: chr4-14144208;