Variant 5-135032710-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002653.5(PITX1):c.169+1003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 216,218 control chromosomes in the GnomAD database, including 5,116 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 0.20 ( 4602 hom., cov: 33)

Exomes 𝑓: 0.11 ( 514 hom. )

Consequence

PITX1
NM_002653.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0250

Variant links:

Genes affected

PITX1 (HGNC:9004): (paired like homeodomain 1) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family are involved in organ development and left-right asymmetry. This protein acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. [provided by RefSeq, Jul 2008]

PITX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PITX1	NM_002653.5 linkuse as main transcript	c.169+1003A>G	intron_variant	ENST00000265340.12
PITX1	XM_047417318.1 linkuse as main transcript	c.271+1003A>G	intron_variant
PITX1	XM_047417319.1 linkuse as main transcript	c.-177+728A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1	ENST00000265340.12 linkuse as main transcript	c.169+1003A>G		intron_variant		1	NM_002653.5	P1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30237

AN:

152104

Hom.:

4567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.0672

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0501

Gnomad FIN

AF:

0.0755

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.107

AC:

6847

AN:

63996

Hom.:

514

AF XY:

0.101

AC XY:

3509

AN XY:

34750

show subpopulations

Gnomad4 AFR exome

AF:

0.445

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.0731

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0543

Gnomad4 FIN exome

AF:

0.0883

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.199

AC:

30345

AN:

152222

Hom.:

4602

Cov.:

AF XY:

0.192

AC XY:

14301

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.424

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.0672

Gnomad4 EAS

AF:

0.00173

Gnomad4 SAS

AF:

0.0513

Gnomad4 FIN

AF:

0.0755

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.0516

Hom.:

Bravo

AF:

0.221

Asia WGS

AF:

0.0520

AC:

182

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over