rs254560

Variant names:

• chr5-135107916-G-A
• rs254560
• ENST00000505828.5:n.280+33388G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-135107916-G-A
• chr5-135107916-G-C
• chr5-135107916-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.330+55394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,166 control chromosomes in the GnomAD database, including 8,811 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 0.32 (8811 hom., cov: 33)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 46 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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.336+55394G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.280+33388G>A		intron	N/A
	PITX1-AS1	ENST00000507641.5	TSL:3	n.429+32528G>A		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.330+55394G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48429 AN: 152048 Hom.: 8806 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.318 AC: 48461 AN: 152166 Hom.: 8811 Cov.: 33 AF XY: 0.318 AC XY: 23666 AN XY: 74370

African (AFR) AF: 0.135 AC: 5623 AN: 41552

American (AMR) AF: 0.357 AC: 5456 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3466

East Asian (EAS) AF: 0.227 AC: 1175 AN: 5184

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4276 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27617 AN: 67966

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.376 Hom.: 46741

Bravo AF: 0.300

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		0.14

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: rs254560;

hg19: chr5-134443606;