3-156754282-C-T

Variant names:

• chr3-156754282-C-T
• rs9822953
• ENST00000472943.6:n.160-3099G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000472943.6(TIPARP-AS1):​n.160-3099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,870 control chromosomes in the GnomAD database, including 28,195 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 0.59 (28195 hom., cov: 30)
• Consequence: TIPARP-AS1 ENST00000472943.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 13 publications found

Genes affected

TIPARP-AS1 (HGNC:41028): (TIPARP antisense RNA 1)

LINC00886 (HGNC:48572): (long intergenic non-protein coding RNA 886)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00886	NR_038387.1	n.177-3099G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIPARP-AS1	ENST00000472943.6	n.160-3099G>A		intron_variant	Intron 1 of 2	2
TIPARP-AS1	ENST00000473352.1	n.177-830G>A		intron_variant	Intron 1 of 1	4
TIPARP-AS1	ENST00000664482.2	n.133-3099G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89761 AN: 151754 Hom.: 28192 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.591 AC: 89787 AN: 151870 Hom.: 28195 Cov.: 30 AF XY: 0.591 AC XY: 43826 AN XY: 74174

African (AFR) AF: 0.373 AC: 15450 AN: 41384

American (AMR) AF: 0.751 AC: 11460 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2449 AN: 3464

East Asian (EAS) AF: 0.846 AC: 4363 AN: 5160

South Asian (SAS) AF: 0.493 AC: 2367 AN: 4798

European-Finnish (FIN) AF: 0.584 AC: 6146 AN: 10532

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45407 AN: 67964

Other (OTH) AF: 0.634 AC: 1334 AN: 2104

Alfa AF: 0.359 Hom.: 868

Bravo AF: 0.601

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9822953; hg19: chr3-156472071;