rs2254209

Positions:

• chr13-38226128-G-C

Variant summary

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

The ENST00000454060.2(LINC00571):​n.388+1890C>G 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 0.171 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 ENST00000454060.2 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00571	ENST00000454060.2	n.388+1890C>G		intron_variant, non_coding_transcript_variant		3
LINC00571	ENST00000451826.2	n.388+1890C>G		intron_variant, non_coding_transcript_variant		2
LINC00571	ENST00000700975.1	n.370+1890C>G		intron_variant, non_coding_transcript_variant

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;