rs1386291

Variant names:

• chr3-150176432-C-T
• rs1386291
• ENST00000487840.6:n.192-36950C>T

Variant summary

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

The ENST00000487840.6(LINC01213):​n.192-36950C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,116 control chromosomes in the GnomAD database, including 4,364 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 0.23 (4364 hom., cov: 33)
• Consequence: LINC01213 ENST00000487840.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 2 publications found

Genes affected

LINC01213 (HGNC:49648): (long intergenic non-protein coding RNA 1213)

ENSG00000241048 (HGNC:):

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 = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01213	ENST00000487840.6	n.192-36950C>T		intron_variant	Intron 2 of 2	2
LINC01213	ENST00000489690.1	n.213-36950C>T		intron_variant	Intron 2 of 2	3
LINC01213	ENST00000716166.1	n.210-39233C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34662 AN: 151998 Hom.: 4358 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.228 AC: 34703 AN: 152116 Hom.: 4364 Cov.: 33 AF XY: 0.224 AC XY: 16661 AN XY: 74362

African (AFR) AF: 0.335 AC: 13900 AN: 41466

American (AMR) AF: 0.206 AC: 3154 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3472

East Asian (EAS) AF: 0.183 AC: 949 AN: 5188

South Asian (SAS) AF: 0.201 AC: 968 AN: 4814

European-Finnish (FIN) AF: 0.135 AC: 1424 AN: 10572

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13013 AN: 67998

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.205 Hom.: 8981

Bravo AF: 0.237

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1386291; hg19: chr3-149894219;