3-150116757-C-T

Variant names:

• chr3-150116757-C-T
• rs10513360
• ENST00000472821.6:n.161-8181C>T

Variant summary

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

The ENST00000487840.6(LINC01213):​n.99-8181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,078 control chromosomes in the GnomAD database, including 672 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 0.082 (672 hom., cov: 32)
• Consequence: LINC01213 ENST00000487840.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 4 publications found

Genes affected

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

LOC105374313 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487840.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374313	NR_136187.1		n.156-8181C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01213	ENST00000472821.6	TSL:3	n.161-8181C>T		intron	N/A
	LINC01213	ENST00000487840.6	TSL:2	n.99-8181C>T		intron	N/A
	LINC01213	ENST00000489690.1	TSL:3	n.120-8181C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12445 AN: 151960 Hom.: 670 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0517

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0655

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

GnomAD4 genome AF: 0.0820 AC: 12465 AN: 152078 Hom.: 672 Cov.: 32 AF XY: 0.0824 AC XY: 6129 AN XY: 74366

African (AFR) AF: 0.141 AC: 5846 AN: 41444

American (AMR) AF: 0.0516 AC: 788 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3472

East Asian (EAS) AF: 0.155 AC: 799 AN: 5166

South Asian (SAS) AF: 0.126 AC: 607 AN: 4804

European-Finnish (FIN) AF: 0.0489 AC: 519 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3487 AN: 67994

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0593 Hom.: 931

Bravo AF: 0.0831

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.1
DANN	Benign	0.71
PhyloP100		0.058

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10513360;

hg19: chr3-149834544;