rs2282424

Variant names:

• chr13-97136192-G-A
• rs2282424
• ENST00000820900.1:n.330+817C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-97136192-G-A
• chr13-97136192-G-C

Variant summary

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

The ENST00000820900.1(LINC00456):​n.330+817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,120 control chromosomes in the GnomAD database, including 870 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 0.099 (870 hom., cov: 32)
• Consequence: LINC00456 ENST00000820900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 4 publications found

Genes affected

LINC00456 (HGNC:42804): (long intergenic non-protein coding RNA 456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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
LINC00456	ENST00000820900.1	n.330+817C>T		intron_variant	Intron 2 of 3
LINC00456	ENST00000820901.1	n.236-14339C>T		intron_variant	Intron 1 of 2
LINC00456	ENST00000820902.1	n.233-14339C>T		intron_variant	Intron 1 of 1
LINC00456	ENST00000820903.1	n.299+817C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0990 AC: 15050 AN: 152002 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0990 AC: 15061 AN: 152120 Hom.: 870 Cov.: 32 AF XY: 0.103 AC XY: 7630 AN XY: 74350

African (AFR) AF: 0.130 AC: 5399 AN: 41516

American (AMR) AF: 0.107 AC: 1636 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.187 AC: 964 AN: 5154

South Asian (SAS) AF: 0.149 AC: 717 AN: 4806

European-Finnish (FIN) AF: 0.0948 AC: 1002 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4681 AN: 68004

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.0749 Hom.: 734

Bravo AF: 0.100

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.40
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs2282424; hg19: chr13-97788446;