4-181156322-G-T

Variant names:

• chr4-181156322-G-T
• rs12503294
• ENST00000512487.2:n.399-583C>A

Variant summary

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

The ENST00000512487.2(LINC00290):​n.399-583C>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 ENST00000512487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512487.2. 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
	LINC00290	NR_033918.1		n.75-583C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00290	ENST00000512487.2	TSL:1	n.399-583C>A		intron	N/A
	LINC00290	ENST00000778348.1		n.161-583C>A		intron	N/A
	LINC00290	ENST00000778349.1		n.109-583C>A		intron	N/A

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

African (AFR) AF: 0.103 AC: 4272 AN: 41464

American (AMR) AF: 0.218 AC: 3323 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0658 AC: 228 AN: 3464

East Asian (EAS) AF: 0.129 AC: 668 AN: 5162

South Asian (SAS) AF: 0.170 AC: 819 AN: 4810

European-Finnish (FIN) AF: 0.144 AC: 1521 AN: 10526

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6068 AN: 67968

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.0943 Hom.: 2228

Bravo AF: 0.116

Asia WGS AF: 0.176 AC: 609 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.22
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs12503294; hg19: chr4-182077475;