rs4871611

chr8-125525328-G-A

Variant summary

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

The ENST00000522815.1(TRIB1AL):n.275-15582G>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 152,100 control chromosomes in the GnomAD database, including 20,979 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 (20979 hom., cov: 32)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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=-0.88).
• 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	UniProt
LINC02964	XR_001746072.2	n.394+2315G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.275-15582G>A		intron_variant, non_coding_transcript_variant		3
TRIB1AL	ENST00000521991.2	n.607+2315G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73294 AN: 151982 Hom.: 20972 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.482 AC: 73303 AN: 152100 Hom.: 20979 Cov.: 32 AF XY: 0.486 AC XY: 36140 AN XY: 74360

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.474

Alfa AF: 0.579 Hom.: 31914

Bravo AF: 0.455

Asia WGS AF: 0.310 AC: 1079 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	0.034
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871611; hg19: chr8-126537570;