rs668103

chr13-38180613-A-C

Variant summary

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

The ENST00000454060.2(LINC00571):n.442+10245T>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 0.338 in 151,938 control chromosomes in the GnomAD database, including 9,023 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 0.34 (9023 hom., cov: 32)
• Consequence: LINC00571 ENST00000454060.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 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.442+10245T>G		intron_variant, non_coding_transcript_variant		3
LINC00571	ENST00000451826.2	n.389-37381T>G		intron_variant, non_coding_transcript_variant		2
LINC00571	ENST00000700975.1	n.424+10245T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51292 AN: 151818 Hom.: 9004 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.338 AC: 51348 AN: 151938 Hom.: 9023 Cov.: 32 AF XY: 0.344 AC XY: 25579 AN XY: 74270

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.330

Alfa AF: 0.352 Hom.: 4951

Bravo AF: 0.329

Asia WGS AF: 0.457 AC: 1588 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.4
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: rs668103; hg19: chr13-38754750;