rs12657484

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.718
Variant links:
Genes affected
PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-AS1NR_161235.1 linkuse as main transcriptn.337-5981T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PITX1-AS1ENST00000624272.3 linkuse as main transcriptn.331-5981T>C intron_variant, non_coding_transcript_variant 2
PITX1-AS1ENST00000505828.5 linkuse as main transcriptn.281-5981T>C intron_variant, non_coding_transcript_variant 4
PITX1-AS1ENST00000513931.2 linkuse as main transcriptn.210-5981T>C intron_variant, non_coding_transcript_variant 3

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12657484; hg19: chr5-134503751; API