rs6982502

Variant names:

• chr8-125467120-C-T
• rs6982502
• ENST00000522815.1:n.95+87C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522815.1(TRIB1AL):​n.95+87C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 42 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.229+87C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.95+87C>T		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 2 AN: 6

East Asian (EAS) AF: 0.357 AC: 5 AN: 14

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 5 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.443 AC: 47 AN: 106

Other (OTH) AF: 0.400 AC: 4 AN: 10

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

African (AFR) AF: 0.863 AC: 35812 AN: 41500

American (AMR) AF: 0.507 AC: 7754 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3464

East Asian (EAS) AF: 0.549 AC: 2840 AN: 5170

South Asian (SAS) AF: 0.469 AC: 2262 AN: 4826

European-Finnish (FIN) AF: 0.552 AC: 5817 AN: 10530

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35598 AN: 67970

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.558 Hom.: 47736

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6982502; hg19: chr8-126479362;