rs1012583

Variant names:

• chr3-150369221-G-A
• rs1012583
• ENST00000716187.1:n.410-27902C>T

Variant summary

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

The ENST00000716187.1(LINC01214):​n.410-27902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,064 control chromosomes in the GnomAD database, including 3,848 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 0.21 (3848 hom., cov: 31)
• Consequence: LINC01214 ENST00000716187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 8 publications found

Genes affected

LINC01214 (HGNC:49650): (long intergenic non-protein coding RNA 1214)

ENSG00000289086 (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 (SAS) allele frequency at 95% confidence interval = 0.354 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
LINC01214	ENST00000716187.1	n.410-27902C>T		intron_variant	Intron 1 of 3
LINC01214	ENST00000716189.1	n.99-3740C>T		intron_variant	Intron 1 of 5
LINC01214	ENST00000716190.1	n.408-3740C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32245 AN: 151946 Hom.: 3851 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.212 AC: 32259 AN: 152064 Hom.: 3848 Cov.: 31 AF XY: 0.213 AC XY: 15859 AN XY: 74336

African (AFR) AF: 0.113 AC: 4683 AN: 41496

American (AMR) AF: 0.221 AC: 3378 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3470

East Asian (EAS) AF: 0.0750 AC: 388 AN: 5176

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4824

European-Finnish (FIN) AF: 0.252 AC: 2657 AN: 10556

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18041 AN: 67950

Other (OTH) AF: 0.197 AC: 415 AN: 2108

Alfa AF: 0.245 Hom.: 14604

Bravo AF: 0.200

Asia WGS AF: 0.217 AC: 754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1012583; hg19: chr3-150087008;