6-134412460-C-T

Position:

• chr6-134412460-C-T

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-24855C>T 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 0.326 in 152,034 control chromosomes in the GnomAD database, including 13,076 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 0.33 (13076 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-24855C>T		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-52281C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49562 AN: 151916 Hom.: 13044 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.326 AC: 49635 AN: 152034 Hom.: 13076 Cov.: 32 AF XY: 0.318 AC XY: 23608 AN XY: 74294

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.333

Alfa AF: 0.248 Hom.: 1021

Bravo AF: 0.354

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726948; hg19: chr6-134733598;