rs372983845

Variant names:

• chr5-135034150-CCCGGCTCCGGCTCCGGCT-C
• NM_002653.5:c.-287_-270delAGCCGGAGCCGGAGCCGG

Your query was ambiguous. Multiple possible variants found:

• chr5-135034150-CCCGGCTCCGGCTCCGGCT-C
• chr5-135034150-CCCGGCTCCGGCTCCGGCT-CCCGGCT
• chr5-135034150-CCCGGCTCCGGCTCCGGCT-CCCGGCTCCGGCT
• chr5-135034150-CCCGGCTCCGGCTCCGGCT-CCCGGCTCCGGCTCCGGCTCCGGCT
• chr5-135034150-CCCGGCTCCGGCTCCGGCT-CCCGGCTCCGGCTCCGGCTCCGGCTCCGGCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_002653.5(PITX1):​c.-287_-270delAGCCGGAGCCGGAGCCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PITX1 NM_002653.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780

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-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX1	NM_002653.5	c.-287_-270delAGCCGGAGCCGGAGCCGG		5_prime_UTR_variant	Exon 1 of 3	ENST00000265340.12	NP_002644.4
PITX1	XM_047417318.1	c.35-219_35-202delAGCCGGAGCCGGAGCCGG		intron_variant	Intron 1 of 3		XP_047273274.1
PITX1-AS1	NR_161235.1	n.267+618_267+635delCGGCTCCGGCTCCGGCTC		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITX1	ENST00000265340.12	c.-287_-270delAGCCGGAGCCGGAGCCGG		5_prime_UTR_variant	Exon 1 of 3	1	NM_002653.5	ENSP00000265340.6

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1760 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1032

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-134369840;