rs489441

Positions:

• chr5-135158291-G-A
• chr5-135158291-G-C
• chr5-135158291-G-T

Variant summary

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

The NR_161235.1(PITX1-AS1):​n.337-15751G>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 0.767 in 152,082 control chromosomes in the GnomAD database, including 45,863 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 0.77 (45863 hom., cov: 31)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITX1-AS1	NR_161235.1	n.337-15751G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.331-15751G>A		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.281-15751G>A		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000513931.2	n.210-15751G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116517 AN: 151964 Hom.: 45800 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.767 AC: 116645 AN: 152082 Hom.: 45863 Cov.: 31 AF XY: 0.766 AC XY: 56960 AN XY: 74344

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.761

Alfa AF: 0.728 Hom.: 9692

Bravo AF: 0.769

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs489441; hg19: chr5-134493981;