rs9543671

Variant names:

• chr13-74527673-C-T
• rs9543671
• ENST00000715466.1:n.86-16167C>T

Variant summary

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

The ENST00000715466.1(LINC00402):​n.86-16167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,020 control chromosomes in the GnomAD database, including 15,772 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 0.43 (15772 hom., cov: 32)
• Consequence: LINC00402 ENST00000715466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 1 publications found

Genes affected

LINC00402 (HGNC:42732): (long intergenic non-protein coding RNA 402)

ENSG00000307743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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
LINC00402	ENST00000715466.1	n.86-16167C>T		intron_variant	Intron 1 of 6
ENSG00000307743	ENST00000828401.1	n.83-23361G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65118 AN: 151902 Hom.: 15768 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.428 AC: 65137 AN: 152020 Hom.: 15772 Cov.: 32 AF XY: 0.429 AC XY: 31882 AN XY: 74300

African (AFR) AF: 0.190 AC: 7878 AN: 41506

American (AMR) AF: 0.416 AC: 6347 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3464

East Asian (EAS) AF: 0.751 AC: 3886 AN: 5176

South Asian (SAS) AF: 0.571 AC: 2752 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5168 AN: 10530

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36038 AN: 67948

Other (OTH) AF: 0.423 AC: 895 AN: 2116

Alfa AF: 0.516 Hom.: 10597

Bravo AF: 0.411

Asia WGS AF: 0.589 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.46
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9543671; hg19: chr13-75101810;