rs10515470

chr5-135297967-T-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.468-35791T>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 0.155 in 147,478 control chromosomes in the GnomAD database, including 1,867 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 0.16 (1867 hom., cov: 33)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITX1-AS1	NR_161235.1	n.468-35791T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.462-35791T>G		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000513931.2	n.435+1378T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 22862 AN: 147362 Hom.: 1868 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.155 AC: 22884 AN: 147478 Hom.: 1867 Cov.: 33 AF XY: 0.153 AC XY: 10941 AN XY: 71654

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0517

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.182

Alfa AF: 0.155 Hom.: 3937

Bravo AF: 0.155

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.2
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515470; hg19: chr5-134633657;