rs254550

chr5-135043267-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161235.1(PITX1-AS1):n.268-9187C>G variant causes a intron, non coding transcript 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 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITX1-AS1	NR_161235.1	n.268-9187C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.262-9187C>G		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.100-9187C>G		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000507641.5	n.160-9187C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0222

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0775

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0946

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	12
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs254550; hg19: chr5-134378957;