rs10507755

Positions:

• chr13-68883858-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038878.1(LINC00550):​n.149+1319A>G variant causes a intron, non coding transcript 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 NR_038878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00550	NR_038878.1	n.149+1319A>G		intron_variant, non_coding_transcript_variant
LINC02342	XR_942055.1	n.86-1195T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02342	ENST00000627910.1	n.90-1195T>C		intron_variant, non_coding_transcript_variant		5
LINC00550	ENST00000629293.1	n.149+1319A>G		intron_variant, non_coding_transcript_variant		1
LINC00550	ENST00000629570.1	n.137+1319A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0856

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.188

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507755; hg19: chr13-69457990;