chr3-150153372-G-A

Variant names:

• chr3-150153372-G-A
• rs2867840
• ENST00000487840.6:n.191+28342G>A

Variant summary

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

The ENST00000487840.6(LINC01213):​n.191+28342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,074 control chromosomes in the GnomAD database, including 3,201 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 0.20 (3201 hom., cov: 32)
• Consequence: LINC01213 ENST00000487840.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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.191+28342G>A		intron_variant	Intron 2 of 2	2
LINC01213	ENST00000489690.1	n.212+28342G>A		intron_variant	Intron 2 of 2	3
LINC01213	ENST00000716166.1	n.209+28342G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30614 AN: 151958 Hom.: 3202 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.201 AC: 30624 AN: 152074 Hom.: 3201 Cov.: 32 AF XY: 0.199 AC XY: 14769 AN XY: 74336

African (AFR) AF: 0.153 AC: 6339 AN: 41504

American (AMR) AF: 0.212 AC: 3235 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3466

East Asian (EAS) AF: 0.145 AC: 750 AN: 5184

South Asian (SAS) AF: 0.273 AC: 1313 AN: 4806

European-Finnish (FIN) AF: 0.163 AC: 1718 AN: 10568

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15814 AN: 67954

Other (OTH) AF: 0.206 AC: 434 AN: 2110

Alfa AF: 0.221 Hom.: 6000

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2867840; hg19: chr3-149871159;