rs1408873

Variant names:

• chr13-46311754-C-T
• rs1408873
• ENST00000826673.1:n.148+9854G>A

Variant summary

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

The ENST00000826673.1(LINC00563):​n.148+9854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 152,150 control chromosomes in the GnomAD database, including 489 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 0.066 (489 hom., cov: 32)
• Consequence: LINC00563 ENST00000826673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826673.1. 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
	LINC00563	ENST00000826673.1		n.148+9854G>A		intron	N/A
	LINC00563	ENST00000826674.1		n.311+5291G>A		intron	N/A
	LINC00563	ENST00000826675.1		n.330+5291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10076 AN: 152030 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0665 AC: 10114 AN: 152150 Hom.: 489 Cov.: 32 AF XY: 0.0681 AC XY: 5068 AN XY: 74370

African (AFR) AF: 0.121 AC: 5003 AN: 41490

American (AMR) AF: 0.102 AC: 1558 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5170

South Asian (SAS) AF: 0.0879 AC: 423 AN: 4814

European-Finnish (FIN) AF: 0.0597 AC: 632 AN: 10590

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0332 AC: 2259 AN: 68006

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0532 Hom.: 115

Bravo AF: 0.0707

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.34
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1408873; hg19: chr13-46885889;