13-46287352-A-T

Variant names:

• chr13-46287352-A-T
• rs1620210
• ENST00000826674.1:n.312-10640T>A

Variant summary

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

The ENST00000826674.1(LINC00563):​n.312-10640T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,134 control chromosomes in the GnomAD database, including 44,229 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 0.75 (44229 hom., cov: 32)
• Consequence: LINC00563 ENST00000826674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 3 publications found

Genes affected

LINC00563 (HGNC:43707): (long intergenic non-protein coding RNA 563)

LOC105370194 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370194	XR_941946.4	n.332-10640T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00563	ENST00000826674.1	n.312-10640T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113939 AN: 152016 Hom.: 44160 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.750 AC: 114067 AN: 152134 Hom.: 44229 Cov.: 32 AF XY: 0.754 AC XY: 56097 AN XY: 74370

African (AFR) AF: 0.935 AC: 38850 AN: 41532

American (AMR) AF: 0.747 AC: 11415 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3470

East Asian (EAS) AF: 0.963 AC: 4985 AN: 5178

South Asian (SAS) AF: 0.796 AC: 3842 AN: 4828

European-Finnish (FIN) AF: 0.653 AC: 6892 AN: 10556

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43042 AN: 67966

Other (OTH) AF: 0.758 AC: 1602 AN: 2114

Alfa AF: 0.594 Hom.: 1814

Bravo AF: 0.766

Asia WGS AF: 0.878 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.46
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1620210; hg19: chr13-46861487;