rs2954029

Positions:

• chr8-125478730-A-T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.274+5416A>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 0.416 in 151,410 control chromosomes in the GnomAD database, including 13,328 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 0.42 (13328 hom., cov: 31)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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
TRIB1AL	ENST00000522815.1	n.274+5416A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62904 AN: 151298 Hom.: 13313 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 62952 AN: 151410 Hom.: 13328 Cov.: 31 AF XY: 0.411 AC XY: 30436 AN XY: 73966

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.423

Alfa AF: 0.459 Hom.: 8899

Bravo AF: 0.409

Asia WGS AF: 0.454 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2954029; hg19: chr8-126490972;