13-62002720-C-T

Variant names:

• chr13-62002720-C-T
• rs10507685
• ENST00000662481.2:n.519+1586G>A

Variant summary

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

The ENST00000662481.2(LINC00358):​n.519+1586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,670 control chromosomes in the GnomAD database, including 3,252 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 0.16 (3252 hom., cov: 31)
• Consequence: LINC00358 ENST00000662481.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

LINC00358 (HGNC:42678): (long intergenic non-protein coding RNA 358)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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
LINC00358	ENST00000662481.2	n.519+1586G>A		intron_variant	Intron 2 of 2
LINC00358	ENST00000834848.1	n.612+1586G>A		intron_variant	Intron 3 of 4
LINC00358	ENST00000834849.1	n.464+1586G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23779 AN: 151552 Hom.: 3233 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.157 AC: 23832 AN: 151670 Hom.: 3252 Cov.: 31 AF XY: 0.156 AC XY: 11587 AN XY: 74114

African (AFR) AF: 0.376 AC: 15526 AN: 41328

American (AMR) AF: 0.0811 AC: 1235 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.0381 AC: 196 AN: 5138

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1064 AN: 10508

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0725 AC: 4923 AN: 67876

Other (OTH) AF: 0.116 AC: 245 AN: 2106

Alfa AF: 0.0549 Hom.: 98

Bravo AF: 0.163

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10507685; hg19: chr13-62576853;