6-134407056-T-A

Position:

• chr6-134407056-T-A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-30259T>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 0.348 in 152,142 control chromosomes in the GnomAD database, including 15,116 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 0.35 (15116 hom., cov: 33)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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.54-30259T>A		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-57685T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52848 AN: 152024 Hom.: 15066 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52940 AN: 152142 Hom.: 15116 Cov.: 33 AF XY: 0.339 AC XY: 25190 AN XY: 74386

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.354

Alfa AF: 0.270 Hom.: 1219

Bravo AF: 0.378

Asia WGS AF: 0.199 AC: 693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321439; hg19: chr6-134728194;