rs12659030

Variant names:

• chr5-135154658-C-T
• rs12659030
• ENST00000505828.5:n.281-19384C>T

Variant summary

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

The ENST00000505828.5(PITX1-AS1):​n.281-19384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,200 control chromosomes in the GnomAD database, including 4,786 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 0.22 (4786 hom., cov: 33)
• Consequence: PITX1-AS1 ENST00000505828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 3 publications found

Genes affected

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.337-19384C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000505828.5	n.281-19384C>T		intron_variant	Intron 3 of 4	4
PITX1-AS1	ENST00000513931.2	n.210-19384C>T		intron_variant	Intron 1 of 3	3
PITX1-AS1	ENST00000624272.3	n.331-19384C>T		intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33632 AN: 152082 Hom.: 4791 Cov.: 33

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.221 AC: 33629 AN: 152200 Hom.: 4786 Cov.: 33 AF XY: 0.222 AC XY: 16523 AN XY: 74406

African (AFR) AF: 0.0789 AC: 3280 AN: 41550

American (AMR) AF: 0.247 AC: 3770 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 894 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3362 AN: 5170

South Asian (SAS) AF: 0.304 AC: 1468 AN: 4828

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10584

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17841 AN: 67984

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.249 Hom.: 3586

Bravo AF: 0.220

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.53
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12659030; hg19: chr5-134490348;