rs4457349

Positions:

• chr8-125482075-A-G
• chr8-125482075-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+8761A>G 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 0.165 in 152,244 control chromosomes in the GnomAD database, including 4,503 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 0.17 (4503 hom., cov: 33)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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+8761A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25123 AN: 152124 Hom.: 4500 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.165 AC: 25154 AN: 152244 Hom.: 4503 Cov.: 33 AF XY: 0.164 AC XY: 12244 AN XY: 74448

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0301

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0551 Hom.: 1469

Bravo AF: 0.183

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4457349; hg19: chr8-126494317;