rs661933

Variant names:

• chr13-38256174-T-C
• rs661933
• ENST00000451826.2:n.323-28091A>G

Variant summary

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

The ENST00000451826.2(LINC00571):​n.323-28091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 152,232 control chromosomes in the GnomAD database, including 195 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 0.034 (195 hom., cov: 32)
• Consequence: LINC00571 ENST00000451826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

LINC00571 (HGNC:43721): (long intergenic non-protein coding RNA 571)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 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
LINC00571	ENST00000451826.2	n.323-28091A>G		intron_variant	Intron 1 of 7	2
LINC00571	ENST00000454060.2	n.323-28091A>G		intron_variant	Intron 1 of 7	3
LINC00571	ENST00000700975.1	n.305-28091A>G		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5121 AN: 152114 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00890

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0337 AC: 5136 AN: 152232 Hom.: 195 Cov.: 32 AF XY: 0.0328 AC XY: 2444 AN XY: 74438

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.00890

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0145 Hom.: 53

Bravo AF: 0.0360

Asia WGS AF: 0.0230 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs661933; hg19: chr13-38830311;