chr3-156775056-C-T

Variant names:

• chr3-156775056-C-T
• rs17380639
• ENST00000472943.6:n.160-23873G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000472943.6(TIPARP-AS1):​n.160-23873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0319 in 152,230 control chromosomes in the GnomAD database, including 113 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 0.032 (113 hom., cov: 32)
• Consequence: TIPARP-AS1 ENST00000472943.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 5 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=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0319 (4863/152230) while in subpopulation NFE AF = 0.0475 (3233/68022). AF 95% confidence interval is 0.0462. There are 113 homozygotes in GnomAd4. There are 2380 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 113 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000472943.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00886	NR_038387.1		n.177-23873G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIPARP-AS1	ENST00000472943.6	TSL:2	n.160-23873G>A		intron	N/A
	TIPARP-AS1	ENST00000473352.1	TSL:4	n.177-21604G>A		intron	N/A
	TIPARP-AS1	ENST00000664482.2		n.133-23873G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4865 AN: 152112 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00867

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0319 AC: 4863 AN: 152230 Hom.: 113 Cov.: 32 AF XY: 0.0320 AC XY: 2380 AN XY: 74434

African (AFR) AF: 0.00864 AC: 359 AN: 41536

American (AMR) AF: 0.0191 AC: 292 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4822

European-Finnish (FIN) AF: 0.0747 AC: 791 AN: 10590

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3233 AN: 68022

Other (OTH) AF: 0.0175 AC: 37 AN: 2116

Alfa AF: 0.0389 Hom.: 270

Bravo AF: 0.0271

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.4
DANN	Benign	0.79
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17380639; hg19: chr3-156492845;