4-181156322-G-T

Variant names:

• chr4-181156322-G-T
• rs12503294
• ENST00000512487.1:n.75-583C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512487.1(LINC00290):​n.75-583C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,968 control chromosomes in the GnomAD database, including 1,131 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 0.11 (1131 hom., cov: 31)
• Consequence: LINC00290 ENST00000512487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

Genes affected

LINC00290 (HGNC:38515): (long intergenic non-protein coding RNA 290)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00290	NR_033918.1	n.75-583C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00290	ENST00000512487.1	n.75-583C>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17180 AN: 151852 Hom.: 1121 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0658

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.113 AC: 17227 AN: 151968 Hom.: 1131 Cov.: 31 AF XY: 0.118 AC XY: 8802 AN XY: 74280

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.0658

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0893

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0916 Hom.: 932

Bravo AF: 0.116

Asia WGS AF: 0.176 AC: 609 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12503294; hg19: chr4-182077475;