rs9493934

chr6-134407424-A-Cchr6-134407424-A-G

Variant summary

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

The ENST00000431422.3(LINC01010):n.54-29891A>C 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 0.284 in 152,114 control chromosomes in the GnomAD database, including 8,996 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 0.28 (8996 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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.54-29891A>C		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-57317A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43123 AN: 151994 Hom.: 8971 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.284 AC: 43188 AN: 152114 Hom.: 8996 Cov.: 32 AF XY: 0.277 AC XY: 20574 AN XY: 74376

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.281

Alfa AF: 0.187 Hom.: 2047

Bravo AF: 0.307

Asia WGS AF: 0.186 AC: 646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.30
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493934; hg19: chr6-134728562;