chr8-125527809-G-A

Position:

• chr8-125527809-G-A

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.275-13101G>A 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 0.482 in 152,102 control chromosomes in the GnomAD database, including 21,013 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 0.48 (21013 hom., cov: 32)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

TRIB1AL (HGNC:56762): (TRIB1 associated lncRNA)

LINC02964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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	UniProt
LINC02964	XR_001746072.2	n.394+4796G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.275-13101G>A		intron_variant, non_coding_transcript_variant		3
TRIB1AL	ENST00000521991.2	n.608-2132G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73366 AN: 151984 Hom.: 21007 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.743

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: 0.482 AC: 73374 AN: 152102 Hom.: 21013 Cov.: 32 AF XY: 0.486 AC XY: 36180 AN XY: 74372

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.474

Alfa AF: 0.588 Hom.: 59789

Bravo AF: 0.456

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.29
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551398; hg19: chr8-126540051;