chr13-38256174-T-C

Variant names:

• chr13-38256174-T-C
• rs661933
• ENST00000451826.2:n.323-28091A>G

Variant summary

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

The ENST00000451826.2(LINC00571):​n.323-28091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 152,232 control chromosomes in the GnomAD database, including 195 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 (195 hom., cov: 32)
• Consequence: LINC00571 ENST00000451826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451826.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00571	ENST00000451826.2	TSL:2	n.323-28091A>G		intron	N/A
	LINC00571	ENST00000454060.2	TSL:3	n.323-28091A>G		intron	N/A
	LINC00571	ENST00000700975.1		n.305-28091A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5121 AN: 152114 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00890

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0337 AC: 5136 AN: 152232 Hom.: 195 Cov.: 32 AF XY: 0.0328 AC XY: 2444 AN XY: 74438

African (AFR) AF: 0.0927 AC: 3850 AN: 41542

American (AMR) AF: 0.0156 AC: 238 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4826

European-Finnish (FIN) AF: 0.00292 AC: 31 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00890 AC: 605 AN: 67998

Other (OTH) AF: 0.0241 AC: 51 AN: 2114

Alfa AF: 0.0152 Hom.: 63

Bravo AF: 0.0360

Asia WGS AF: 0.0230 AC: 78 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs661933; hg19: chr13-38830311;