6-134411396-T-G

Variant names:

• chr6-134411396-T-G
• rs9493942
• ENST00000431422.3:n.54-25919T>G

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-25919T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,144 control chromosomes in the GnomAD database, including 14,778 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 0.34 (14778 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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.54-25919T>G		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.54-53345T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51911 AN: 152026 Hom.: 14730 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.342 AC: 52001 AN: 152144 Hom.: 14778 Cov.: 32 AF XY: 0.333 AC XY: 24749 AN XY: 74382

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.347

Alfa AF: 0.214 Hom.: 4495

Bravo AF: 0.372

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9493942; hg19: chr6-134732534;