rs12657484

Positions:

• chr5-135168061-T-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.337-5981T>C 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 0.25 in 151,702 control chromosomes in the GnomAD database, including 6,002 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 0.25 (6002 hom., cov: 31)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITX1-AS1	NR_161235.1	n.337-5981T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.331-5981T>C		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.281-5981T>C		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000513931.2	n.210-5981T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37873 AN: 151584 Hom.: 6004 Cov.: 31

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.250 AC: 37878 AN: 151702 Hom.: 6002 Cov.: 31 AF XY: 0.253 AC XY: 18722 AN XY: 74104

Gnomad4 AFR AF: 0.0806

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.250

Alfa AF: 0.293 Hom.: 3759

Bravo AF: 0.248

Asia WGS AF: 0.460 AC: 1598 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	6.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12657484; hg19: chr5-134503751;