rs34727399

Variant names:

• chr7-56011528-CAAAA-C
• NM_004577.4:c.*230_*233delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr7-56011528-CAAAA-C
• chr7-56011528-CAAAA-CA
• chr7-56011528-CAAAA-CAA
• chr7-56011528-CAAAA-CAAA
• chr7-56011528-CAAAA-CAAAAA
• chr7-56011528-CAAAA-CAAAAAA
• chr7-56011528-CAAAA-CAAAAAAA
• chr7-56011528-CAAAA-CAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004577.4(PSPH):​c.*230_*233delTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000196 in 102,272 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000020 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PSPH NM_004577.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

PSPH (HGNC:9577): (phosphoserine phosphatase) The protein encoded by this gene belongs to a subfamily of the phosphotransferases. This encoded enzyme is responsible for the third and last step in L-serine formation. It catalyzes magnesium-dependent hydrolysis of L-phosphoserine and is also involved in an exchange reaction between L-serine and L-phosphoserine. Deficiency of this protein is thought to be linked to Williams syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSPH	NM_004577.4	c.*230_*233delTTTT		3_prime_UTR_variant	Exon 8 of 8	ENST00000275605.8	NP_004568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSPH	ENST00000275605	c.*230_*233delTTTT		3_prime_UTR_variant	Exon 8 of 8	1	NM_004577.4	ENSP00000275605.3
PSPH	ENST00000395471	c.*230_*233delTTTT		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000378854.3
PSPH	ENST00000437355.6	n.*218+12_*218+15delTTTT		intron_variant	Intron 6 of 6	5		ENSP00000401639.2
PSPH	ENST00000459834.5	n.*6_*9delTTTT		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 123568 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000196 AC: 2 AN: 102272 Hom.: 0 AF XY: 0.0000176 AC XY: 1 AN XY: 56918

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: 0.000227

Gnomad4 NFE exome AF: 0.0000165

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 123568 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 59084

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-56079221;