chr13-68883858-T-C

Variant names:

• chr13-68883858-T-C
• rs10507755
• ENST00000629293.1:n.149+1319A>G

Variant summary

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

The ENST00000629293.1(LINC00550):​n.149+1319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,944 control chromosomes in the GnomAD database, including 2,404 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 0.17 (2404 hom., cov: 32)
• Consequence: LINC00550 ENST00000629293.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 2 publications found

Genes affected

LINC00550 (HGNC:43688): (long intergenic non-protein coding RNA 550)

LINC02342 (HGNC:53262): (long intergenic non-protein coding RNA 2342)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629293.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00550	NR_038878.1		n.149+1319A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00550	ENST00000629293.1	TSL:1	n.149+1319A>G		intron	N/A
	LINC02342	ENST00000627910.1	TSL:5	n.90-1195T>C		intron	N/A
	LINC00550	ENST00000629570.2	TSL:3	n.140+1319A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25300 AN: 151826 Hom.: 2401 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.167 AC: 25332 AN: 151944 Hom.: 2404 Cov.: 32 AF XY: 0.163 AC XY: 12076 AN XY: 74278

African (AFR) AF: 0.124 AC: 5144 AN: 41472

American (AMR) AF: 0.166 AC: 2531 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3468

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5172

South Asian (SAS) AF: 0.0856 AC: 412 AN: 4812

European-Finnish (FIN) AF: 0.158 AC: 1670 AN: 10558

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13948 AN: 67890

Other (OTH) AF: 0.188 AC: 396 AN: 2110

Alfa AF: 0.180 Hom.: 345

Bravo AF: 0.167

Asia WGS AF: 0.0600 AC: 208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.60
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs10507755; hg19: chr13-69457990;