rs10808546

Variant names:

• chr8-125483576-C-T
• rs10808546
• ENST00000522815.1:n.274+10262C>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+10262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,842 control chromosomes in the GnomAD database, including 11,433 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 0.38 (11433 hom., cov: 31)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 49 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 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+10262C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+10262C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57666 AN: 151724 Hom.: 11423 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.380 AC: 57714 AN: 151842 Hom.: 11433 Cov.: 31 AF XY: 0.372 AC XY: 27608 AN XY: 74220

African (AFR) AF: 0.336 AC: 13910 AN: 41398

American (AMR) AF: 0.311 AC: 4742 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3464

East Asian (EAS) AF: 0.121 AC: 623 AN: 5164

South Asian (SAS) AF: 0.232 AC: 1114 AN: 4812

European-Finnish (FIN) AF: 0.436 AC: 4573 AN: 10498

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30133 AN: 67922

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.417 Hom.: 39859

Bravo AF: 0.371

Asia WGS AF: 0.204 AC: 713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.42
PhyloP100		-0.26

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: rs10808546;

hg19: chr8-126495818;