5-135227467-C-T

Variant names:

• chr5-135227467-C-T
• rs634308
• ENST00000513931.2:n.340+53295C>T

Variant summary

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

The ENST00000513931.2(PITX1-AS1):​n.340+53295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,120 control chromosomes in the GnomAD database, including 31,770 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 0.65 (31770 hom., cov: 33)
• Consequence: PITX1-AS1 ENST00000513931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.661 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.467+53295C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000513931.2	TSL:3	n.340+53295C>T		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.461+53295C>T		intron	N/A
	PITX1-AS1	ENST00000782562.1		n.211-26482C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98058 AN: 152000 Hom.: 31741 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.645 AC: 98138 AN: 152120 Hom.: 31770 Cov.: 33 AF XY: 0.645 AC XY: 47962 AN XY: 74370

African (AFR) AF: 0.610 AC: 25311 AN: 41488

American (AMR) AF: 0.668 AC: 10222 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1979 AN: 3466

East Asian (EAS) AF: 0.658 AC: 3393 AN: 5160

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4812

European-Finnish (FIN) AF: 0.693 AC: 7341 AN: 10596

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45307 AN: 67988

Other (OTH) AF: 0.648 AC: 1367 AN: 2108

Alfa AF: 0.660 Hom.: 112953

Bravo AF: 0.646

Asia WGS AF: 0.590 AC: 2054 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	5.1
DANN	Benign	0.85
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs634308; hg19: chr5-134563157;