13-54241971-G-C

Variant names:

• chr13-54241971-G-C
• rs7335975
• ENST00000706987.1:n.534C>G

Variant summary

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

The ENST00000706987.1(LINC00458):​n.534C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,922 control chromosomes in the GnomAD database, including 2,208 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 0.14 (2208 hom., cov: 33)
• Consequence: LINC00458 ENST00000706987.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 1 publications found

Genes affected

LINC00458 (HGNC:42807): (long intergenic non-protein coding RNA 458)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706987.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00458	ENST00000706987.1		n.534C>G		non_coding_transcript_exon	Exon 3 of 3
	LINC00458	ENST00000706988.1		n.1652C>G		non_coding_transcript_exon	Exon 3 of 3
	LINC00458	ENST00000706980.1		n.119+27271C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21308 AN: 151804 Hom.: 2208 Cov.: 33

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.140 AC: 21317 AN: 151922 Hom.: 2208 Cov.: 33 AF XY: 0.148 AC XY: 10993 AN XY: 74232

African (AFR) AF: 0.0427 AC: 1771 AN: 41482

American (AMR) AF: 0.177 AC: 2689 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2581 AN: 5120

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4826

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10580

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 9957 AN: 67918

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.0670 Hom.: 93

Bravo AF: 0.132

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.2
DANN	Benign	0.56
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs7335975; hg19: chr13-54816106;