rs4457349

Variant names:

• chr8-125482075-A-G
• rs4457349
• ENST00000522815.1:n.274+8761A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-125482075-A-G
• chr8-125482075-A-T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.274+8761A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 6 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522815.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	NR_186610.1		n.408+8761A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+8761A>G		intron	N/A

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

African (AFR) AF: 0.427 AC: 17727 AN: 41486

American (AMR) AF: 0.109 AC: 1673 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2102 AN: 5182

South Asian (SAS) AF: 0.189 AC: 912 AN: 4834

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2049 AN: 68022

Other (OTH) AF: 0.141 AC: 299 AN: 2116

Alfa AF: 0.0738 Hom.: 5741

Bravo AF: 0.183

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.72
PhyloP100		0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4457349;

hg19: chr8-126494317;