rs686712

Variant names:

• chr13-38256740-G-A
• rs686712
• ENST00000451826.2:n.323-28657C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451826.2(LINC00571):​n.323-28657C>T variant causes a intron 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 ENST00000451826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 0 publications found

Genes affected

LINC00571 (HGNC:43721): (long intergenic non-protein coding RNA 571)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000451826.2	n.323-28657C>T		intron_variant	Intron 1 of 7	2
LINC00571	ENST00000454060.2	n.323-28657C>T		intron_variant	Intron 1 of 7	3
LINC00571	ENST00000700975.1	n.305-28657C>T		intron_variant	Intron 1 of 8

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

African (AFR) AF: 0.0934 AC: 3872 AN: 41472

American (AMR) AF: 0.0156 AC: 239 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0387 AC: 186 AN: 4812

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10582

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00887 AC: 603 AN: 67996

Other (OTH) AF: 0.0242 AC: 51 AN: 2110

Alfa AF: 0.0251 Hom.: 18

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs686712; hg19: chr13-38830877;