rs6982636

chr8-125467073-G-Achr8-125467073-G-C

Variant summary

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

The ENST00000522815.1(TRIB1AL):n.95+40G>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 0.428 in 152,034 control chromosomes in the GnomAD database, including 14,131 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 0.43 (14110 hom., cov: 31)
  • Exomes 𝑓: 0.49 (21 hom.)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

TRIB1AL (HGNC:56762): (TRIB1 associated lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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
TRIB1AL	ENST00000522815.1	n.95+40G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64973 AN: 151758 Hom.: 14089 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.419

GnomAD4 exome AF: 0.494 AC: 78 AN: 158 Hom.: 21 Cov.: 0 AF XY: 0.427 AC XY: 35 AN XY: 82

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.583

GnomAD4 genome AF: 0.428 AC: 65032 AN: 151876 Hom.: 14110 Cov.: 31 AF XY: 0.423 AC XY: 31393 AN XY: 74198

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.426

Alfa AF: 0.447 Hom.: 7579

Bravo AF: 0.422

Asia WGS AF: 0.460 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.014
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6982636; hg19: chr8-126479315;