rs686712

Positions:

• chr13-38256740-G-A

Variant summary

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

The ENST00000454060.2(LINC00571):​n.323-28657C>T 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 0.0339 in 152,106 control chromosomes in the GnomAD database, including 196 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 0.034 (196 hom., cov: 31)
• Consequence: LINC00571 ENST00000454060.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0909 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.323-28657C>T		intron_variant, non_coding_transcript_variant		3
LINC00571	ENST00000451826.2	n.323-28657C>T		intron_variant, non_coding_transcript_variant		2
LINC00571	ENST00000700975.1	n.305-28657C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5140 AN: 151988 Hom.: 196 Cov.: 31

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0390

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00887

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0339 AC: 5155 AN: 152106 Hom.: 196 Cov.: 31 AF XY: 0.0329 AC XY: 2446 AN XY: 74342

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.00887

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0225 Hom.: 16

Bravo AF: 0.0363

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686712; hg19: chr13-38830877;