chr13-87752832-C-T

Variant names:

• chr13-87752832-C-T
• rs7325257
• ENST00000717718.1:n.67-37338G>A

Variant summary

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

The ENST00000717718.1(LINC00397):​n.67-37338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,700 control chromosomes in the GnomAD database, including 19,176 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 0.48 (19176 hom., cov: 31)
• Consequence: LINC00397 ENST00000717718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836
• Publications: 4 publications found

Genes affected

LINC00397 (HGNC:42725): (long intergenic non-protein coding RNA 397)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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
LINC00397	ENST00000717718.1	n.67-37338G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73367 AN: 151582 Hom.: 19123 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.484 AC: 73478 AN: 151700 Hom.: 19176 Cov.: 31 AF XY: 0.492 AC XY: 36504 AN XY: 74130

African (AFR) AF: 0.599 AC: 24781 AN: 41396

American (AMR) AF: 0.447 AC: 6793 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3468

East Asian (EAS) AF: 0.973 AC: 5004 AN: 5142

South Asian (SAS) AF: 0.604 AC: 2913 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5027 AN: 10528

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25910 AN: 67830

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.421 Hom.: 51631

Bravo AF: 0.488

Asia WGS AF: 0.776 AC: 2693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.8
DANN	Benign	0.85
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs7325257; hg19: chr13-88405087;