rs10515470

Variant names:

• chr5-135297967-T-G
• rs10515470
• ENST00000513931.2:n.435+1378T>G

Variant summary

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

The ENST00000513931.2(PITX1-AS1):​n.435+1378T>G variant causes a intron 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 ENST00000513931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 4 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=-0.88).
• 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 rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.468-35791T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000513931.2	n.435+1378T>G		intron_variant	Intron 3 of 3	3
PITX1-AS1	ENST00000624272.3	n.462-35791T>G		intron_variant	Intron 3 of 5	2
PITX1-AS1	ENST00000782562.1	n.369+1378T>G		intron_variant	Intron 4 of 5
PITX1-AS1	ENST00000782563.1	n.466-13568T>G		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.190 AC: 7554 AN: 39708

American (AMR) AF: 0.130 AC: 1901 AN: 14598

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 692 AN: 3444

East Asian (EAS) AF: 0.0517 AC: 253 AN: 4894

South Asian (SAS) AF: 0.109 AC: 485 AN: 4440

European-Finnish (FIN) AF: 0.114 AC: 1149 AN: 10042

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10275 AN: 67142

Other (OTH) AF: 0.182 AC: 367 AN: 2020

Alfa AF: 0.155 Hom.: 7167

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10515470; hg19: chr5-134633657;