rs1770329

Variant names:

• chr13-68850809-T-C
• rs1770329
• ENST00000841937.1:n.170+34368A>G

Variant summary

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

The ENST00000841937.1(LINC00550):​n.170+34368A>G 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 151,964 control chromosomes in the GnomAD database, including 4,167 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 (4167 hom., cov: 32)
• Consequence: LINC00550 ENST00000841937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00550	ENST00000841937.1	n.170+34368A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33948 AN: 151846 Hom.: 4160 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.224 AC: 33992 AN: 151964 Hom.: 4167 Cov.: 32 AF XY: 0.219 AC XY: 16246 AN XY: 74276

African (AFR) AF: 0.187 AC: 7768 AN: 41484

American (AMR) AF: 0.198 AC: 3022 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1087 AN: 3464

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5178

South Asian (SAS) AF: 0.104 AC: 499 AN: 4816

European-Finnish (FIN) AF: 0.239 AC: 2527 AN: 10590

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

European-Non Finnish (NFE) AF: 0.270 AC: 18346 AN: 67862

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.239 Hom.: 596

Bravo AF: 0.221

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1770329; hg19: chr13-69424941;