rs254551

Variant names:

• chr5-135044841-G-A
• rs254551
• ENST00000505828.5:n.100-7613G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-135044841-G-A
• chr5-135044841-G-C
• chr5-135044841-G-T

Variant summary

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

The ENST00000624272.3(PITX1-AS1):​n.262-7613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,938 control chromosomes in the GnomAD database, including 13,011 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 0.40 (13011 hom., cov: 32)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 6 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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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.268-7613G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.100-7613G>A		intron	N/A
	PITX1-AS1	ENST00000507641.5	TSL:3	n.160-7613G>A		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.262-7613G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61434 AN: 151820 Hom.: 12994 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.405 AC: 61483 AN: 151938 Hom.: 13011 Cov.: 32 AF XY: 0.407 AC XY: 30205 AN XY: 74232

African (AFR) AF: 0.283 AC: 11723 AN: 41474

American (AMR) AF: 0.486 AC: 7425 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3468

East Asian (EAS) AF: 0.512 AC: 2629 AN: 5134

South Asian (SAS) AF: 0.511 AC: 2458 AN: 4806

European-Finnish (FIN) AF: 0.450 AC: 4748 AN: 10542

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29867 AN: 67916

Other (OTH) AF: 0.406 AC: 857 AN: 2110

Alfa AF: 0.432 Hom.: 64435

Bravo AF: 0.401

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-1.8

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: rs254551;

hg19: chr5-134380531;

COSMIC: COSV71405547;