rs9402592

chr6-134398929-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-38386G>A		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.53+55570G>A		intron_variant, non_coding_transcript_variant

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;