rs2603014

Variant names:

• chr5-135307426-T-C
• rs2603014
• ENST00000513931.2:n.435+10837T>C

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+10837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,964 control chromosomes in the GnomAD database, including 16,610 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 0.45 (16610 hom., cov: 32)
• Consequence: PITX1-AS1 ENST00000513931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.468-26332T>C		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+10837T>C		intron_variant	Intron 3 of 3	3
PITX1-AS1	ENST00000624272.3	n.462-26332T>C		intron_variant	Intron 3 of 5	2
PITX1-AS1	ENST00000782562.1	n.369+10837T>C		intron_variant	Intron 4 of 5
PITX1-AS1	ENST00000782563.1	n.466-4109T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67696 AN: 151846 Hom.: 16584 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.446 AC: 67770 AN: 151964 Hom.: 16610 Cov.: 32 AF XY: 0.438 AC XY: 32569 AN XY: 74284

African (AFR) AF: 0.650 AC: 26952 AN: 41452

American (AMR) AF: 0.430 AC: 6562 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.136 AC: 702 AN: 5148

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4812

European-Finnish (FIN) AF: 0.286 AC: 3019 AN: 10554

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26191 AN: 67946

Other (OTH) AF: 0.454 AC: 957 AN: 2106

Alfa AF: 0.401 Hom.: 23632

Bravo AF: 0.466

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.33
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2603014; hg19: chr5-134643116;