rs624839

chr13-38270788-A-G

Variant summary

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

The ENST00000454060.2(LINC00571):n.323-42705T>C 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 0.0747 in 152,246 control chromosomes in the GnomAD database, including 1,160 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 0.075 (1160 hom., cov: 32)
• Consequence: LINC00571 ENST00000454060.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

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 = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00571	ENST00000454060.2	n.323-42705T>C		intron_variant, non_coding_transcript_variant		3
LINC00571	ENST00000451826.2	n.323-42705T>C		intron_variant, non_coding_transcript_variant		2
LINC00571	ENST00000700975.1	n.305-42705T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11321 AN: 152128 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.00282

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00942

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0747 AC: 11367 AN: 152246 Hom.: 1160 Cov.: 32 AF XY: 0.0722 AC XY: 5372 AN XY: 74440

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.00282

Gnomad4 NFE AF: 0.00942

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0305 Hom.: 138

Bravo AF: 0.0840

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.3
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624839; hg19: chr13-38844925;