rs9493934

Variant names:

• chr6-134407424-A-C
• rs9493934
• ENST00000431422.3:n.54-29891A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-134407424-A-C
• chr6-134407424-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-29891A>C		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.54-57317A>C		intron_variant	Intron 1 of 2

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;