rs2254209

Variant names:

• chr13-38226128-G-C
• rs2254209
• ENST00000451826.2:n.388+1890C>G

Variant summary

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

The ENST00000451826.2(LINC00571):​n.388+1890C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,644 control chromosomes in the GnomAD database, including 2,364 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 (2364 hom., cov: 32)
• Consequence: LINC00571 ENST00000451826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 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.388+1890C>G		intron_variant	Intron 2 of 7	2
LINC00571	ENST00000454060.2	n.388+1890C>G		intron_variant	Intron 2 of 7	3
LINC00571	ENST00000700975.1	n.370+1890C>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25864 AN: 151526 Hom.: 2365 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.171 AC: 25860 AN: 151644 Hom.: 2364 Cov.: 32 AF XY: 0.170 AC XY: 12598 AN XY: 74124

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.183

Alfa AF: 0.170 Hom.: 290

Bravo AF: 0.165

Asia WGS AF: 0.105 AC: 363 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2254209; hg19: chr13-38800265;