rs254560

Positions:

• chr5-135107916-G-A
• chr5-135107916-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161235.1(PITX1-AS1):​n.336+55394G>A 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 0.318 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 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.336+55394G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.330+55394G>A		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.280+33388G>A		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000507641.5	n.429+32528G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.332

Alfa AF: 0.385 Hom.: 21069

Bravo AF: 0.300

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs254560; hg19: chr5-134443606;