rs6982502

chr8-125467120-C-T

Variant summary

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

The ENST00000522815.1(TRIB1AL):n.95+87C>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 0.615 in 152,206 control chromosomes in the GnomAD database, including 30,576 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 0.61 (30562 hom., cov: 31)
  • Exomes 𝑓: 0.44 (14 hom.)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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+87C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93378 AN: 151934 Hom.: 30503 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.442 AC: 68 AN: 154 Hom.: 14 AF XY: 0.378 AC XY: 31 AN XY: 82

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.357

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.443

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.615 AC: 93491 AN: 152052 Hom.: 30562 Cov.: 31 AF XY: 0.610 AC XY: 45311 AN XY: 74330

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.569

Alfa AF: 0.529 Hom.: 28940

Bravo AF: 0.621

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.093
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6982502; hg19: chr8-126479362;