rs9402592

Variant names:

• chr6-134398929-G-A
• rs9402592
• ENST00000431422.3:n.54-38386G>A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-38386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,808 control chromosomes in the GnomAD database, including 16,417 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 (16417 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 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
LINC01010	ENST00000431422.3	n.54-38386G>A		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.53+55570G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65216 AN: 151690 Hom.: 16404 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.430 AC: 65243 AN: 151808 Hom.: 16417 Cov.: 32 AF XY: 0.439 AC XY: 32561 AN XY: 74188

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.416

Alfa AF: 0.505 Hom.: 24514

Bravo AF: 0.413

Asia WGS AF: 0.564 AC: 1957 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9402592; hg19: chr6-134720067;