rs624839

Variant names:

• chr13-38270788-A-G
• rs624839
• ENST00000451826.2:n.323-42705T>C

Variant summary

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

The ENST00000451826.2(LINC00571):​n.323-42705T>C variant causes a intron 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 ENST00000451826.2 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000451826.2	n.323-42705T>C		intron_variant	Intron 1 of 7	2
LINC00571	ENST00000454060.2	n.323-42705T>C		intron_variant	Intron 1 of 7	3
LINC00571	ENST00000700975.1	n.305-42705T>C		intron_variant	Intron 1 of 8

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;