chr5-135329392-G-T

Variant names:

• chr5-135329392-G-T
• rs13163460
• ENST00000513931.2:n.436-8543G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000513931.2(PITX1-AS1):​n.436-8543G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,180 control chromosomes in the GnomAD database, including 10,580 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 0.31 (10580 hom., cov: 33)
• Consequence: PITX1-AS1 ENST00000513931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513931.2. 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
	PITX1-AS1	NR_161235.1		n.468-4366G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000513931.2	TSL:3	n.436-8543G>T		intron	N/A
	PITX1-AS1	ENST00000555438.3	TSL:3	n.159+5152G>T		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.462-4366G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47620 AN: 152062 Hom.: 10526 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.314 AC: 47734 AN: 152180 Hom.: 10580 Cov.: 33 AF XY: 0.308 AC XY: 22893 AN XY: 74396

African (AFR) AF: 0.629 AC: 26096 AN: 41494

American (AMR) AF: 0.254 AC: 3892 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3470

East Asian (EAS) AF: 0.153 AC: 795 AN: 5182

South Asian (SAS) AF: 0.203 AC: 979 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1500 AN: 10610

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12633 AN: 68002

Other (OTH) AF: 0.301 AC: 636 AN: 2110

Alfa AF: 0.217 Hom.: 8686

Bravo AF: 0.337

Asia WGS AF: 0.214 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.7
DANN	Benign	0.87
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs13163460; hg19: chr5-134665082;