5-135158291-G-A

Variant names:

• chr5-135158291-G-A
• rs489441
• ENST00000505828.5:n.281-15751G>A

Variant summary

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

The ENST00000624272.3(PITX1-AS1):​n.331-15751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,082 control chromosomes in the GnomAD database, including 45,863 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 0.77 (45863 hom., cov: 31)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624272.3. 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.337-15751G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.281-15751G>A		intron	N/A
	PITX1-AS1	ENST00000513931.2	TSL:3	n.210-15751G>A		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.331-15751G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116517 AN: 151964 Hom.: 45800 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.767 AC: 116645 AN: 152082 Hom.: 45863 Cov.: 31 AF XY: 0.766 AC XY: 56960 AN XY: 74344

African (AFR) AF: 0.924 AC: 38322 AN: 41480

American (AMR) AF: 0.748 AC: 11447 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2534 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1814 AN: 5156

South Asian (SAS) AF: 0.687 AC: 3305 AN: 4814

European-Finnish (FIN) AF: 0.758 AC: 8023 AN: 10578

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48659 AN: 67968

Other (OTH) AF: 0.761 AC: 1609 AN: 2114

Alfa AF: 0.726 Hom.: 22080

Bravo AF: 0.769

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.72
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs489441; hg19: chr5-134493981;