rs4366580

Variant names:

• chr13-22860923-C-T
• rs4366580
• ENST00000663150.1:n.966-1012G>A

Variant summary

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

The ENST00000663150.1(LINC00621):​n.966-1012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,128 control chromosomes in the GnomAD database, including 2,597 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 (2597 hom., cov: 33)
• Consequence: LINC00621 ENST00000663150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

Genes affected

LINC00621 (HGNC:44227): (long intergenic non-protein coding RNA 621)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 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
LINC00621	ENST00000663150.1	n.966-1012G>A		intron_variant	Intron 4 of 4
LINC00621	ENST00000668623.1	n.1151-1012G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25613 AN: 152008 Hom.: 2595 Cov.: 33

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.168 AC: 25631 AN: 152128 Hom.: 2597 Cov.: 33 AF XY: 0.173 AC XY: 12898 AN XY: 74354

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.188

Alfa AF: 0.198 Hom.: 4962

Bravo AF: 0.166

Asia WGS AF: 0.205 AC: 708 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4366580; hg19: chr13-23435062;