5-135163402-C-A

Variant names:

• chr5-135163402-C-A
• rs647161
• ENST00000505828.5:n.281-10640C>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.331-10640C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,018 control chromosomes in the GnomAD database, including 30,260 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 0.63 (30260 hom., cov: 32)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 75 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=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	NR_161235.1		n.337-10640C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.281-10640C>A		intron	N/A
	PITX1-AS1	ENST00000513931.2	TSL:3	n.210-10640C>A		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.331-10640C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95130 AN: 151900 Hom.: 30240 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.626 AC: 95171 AN: 152018 Hom.: 30260 Cov.: 32 AF XY: 0.628 AC XY: 46680 AN XY: 74330

African (AFR) AF: 0.559 AC: 23189 AN: 41450

American (AMR) AF: 0.632 AC: 9657 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2463 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5162

South Asian (SAS) AF: 0.627 AC: 3016 AN: 4812

European-Finnish (FIN) AF: 0.691 AC: 7323 AN: 10592

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45549 AN: 67934

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.645 Hom.: 59122

Bravo AF: 0.616

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs647161; hg19: chr5-134499092;