rs921720

Positions:

• chr8-125522429-A-G

Variant summary

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

The ENST00000521991.2(ENSG00000253111):​n.281-258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,046 control chromosomes in the GnomAD database, including 21,159 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 0.49 (21159 hom., cov: 31)
• Consequence: ENSG00000253111 ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

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

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.409-18481A>G		intron_variant
LINC02964	XR_001746072.2	n.124-314A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253111	ENST00000521991.2	n.281-258A>G		intron_variant		2
ENSG00000253111	ENST00000522815.1	n.275-18481A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73809 AN: 151928 Hom.: 21155 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.485 AC: 73814 AN: 152046 Hom.: 21159 Cov.: 31 AF XY: 0.490 AC XY: 36397 AN XY: 74326

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.474

Alfa AF: 0.577 Hom.: 26148

Bravo AF: 0.458

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.066
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921720; hg19: chr8-126534671;