5-135043267-C-G

Variant names:

• chr5-135043267-C-G
• rs254550
• ENST00000505828.5:n.100-9187C>G

Variant summary

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

The ENST00000624272.3(PITX1-AS1):​n.262-9187C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 152,270 control chromosomes in the GnomAD database, including 641 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 0.080 (641 hom., cov: 33)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 1 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=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 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.268-9187C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.100-9187C>G		intron	N/A
	PITX1-AS1	ENST00000507641.5	TSL:3	n.160-9187C>G		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.262-9187C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12207 AN: 152152 Hom.: 633 Cov.: 33

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.0803 AC: 12234 AN: 152270 Hom.: 641 Cov.: 33 AF XY: 0.0781 AC XY: 5811 AN XY: 74444

African (AFR) AF: 0.0222 AC: 923 AN: 41562

American (AMR) AF: 0.153 AC: 2347 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.0505 AC: 243 AN: 4812

European-Finnish (FIN) AF: 0.0775 AC: 821 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7441 AN: 68024

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0905 Hom.: 101

Bravo AF: 0.0843

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs254550;

hg19: chr5-134378957;