rs9402592

Variant names:

• chr6-134398929-G-A
• rs9402592
• ENST00000792719.1:n.1518G>A

Variant summary

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

The ENST00000792719.1(LINC01010):​n.1518G>A variant causes a non coding transcript exon 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 ENST00000792719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000792719.1	n.1518G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01010	ENST00000792720.1	n.1586G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01010	ENST00000431422.3	n.54-38386G>A		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.152 AC: 6281 AN: 41380

American (AMR) AF: 0.562 AC: 8573 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2873 AN: 5160

South Asian (SAS) AF: 0.581 AC: 2802 AN: 4826

European-Finnish (FIN) AF: 0.583 AC: 6124 AN: 10504

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35871 AN: 67918

Other (OTH) AF: 0.416 AC: 875 AN: 2104

Alfa AF: 0.489 Hom.: 60045

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9402592; hg19: chr6-134720067;