rs661827

Variant names:

• chr13-68850619-C-A
• rs661827
• ENST00000841937.1:n.170+34558G>T

Variant summary

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

The ENST00000841937.1(LINC00550):​n.170+34558G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,956 control chromosomes in the GnomAD database, including 4,168 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 0.22 (4168 hom., cov: 32)
• Consequence: LINC00550 ENST00000841937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 4 publications found

Genes affected

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

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 (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841937.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00550	ENST00000841937.1		n.170+34558G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33958 AN: 151838 Hom.: 4161 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.224 AC: 34002 AN: 151956 Hom.: 4168 Cov.: 32 AF XY: 0.219 AC XY: 16235 AN XY: 74252

African (AFR) AF: 0.187 AC: 7773 AN: 41490

American (AMR) AF: 0.199 AC: 3030 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3464

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5174

South Asian (SAS) AF: 0.104 AC: 501 AN: 4828

European-Finnish (FIN) AF: 0.238 AC: 2510 AN: 10568

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18350 AN: 67860

Other (OTH) AF: 0.243 AC: 513 AN: 2112

Alfa AF: 0.257 Hom.: 19746

Bravo AF: 0.221

Asia WGS AF: 0.0670 AC: 235 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	0.16
DANN	Benign	0.48
PhyloP100		-0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs661827;

hg19: chr13-69424751;