rs2954038

Variant names:

• chr8-125495147-C-A
• rs2954038
• ENST00000521991.2:n.280+8188C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-125495147-C-A
• chr8-125495147-C-G

Variant summary

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

The ENST00000521991.2(ENSG00000253111):​n.280+8188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,214 control chromosomes in the GnomAD database, including 44,483 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 0.76 (44483 hom., cov: 33)
• Consequence: ENSG00000253111 ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

ENSG00000253111 (HGNC:56762): (TRIB1 associated lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.408+21833C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253111	ENST00000521991.2	n.280+8188C>A		intron_variant	Intron 1 of 2	2
ENSG00000253111	ENST00000522815.1	n.274+21833C>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115373 AN: 152096 Hom.: 44422 Cov.: 33

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.759 AC: 115491 AN: 152214 Hom.: 44483 Cov.: 33 AF XY: 0.759 AC XY: 56443 AN XY: 74406

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.700

Alfa AF: 0.699 Hom.: 43202

Bravo AF: 0.763

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.066
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2954038; hg19: chr8-126507389;