NM_019042.5:c.-32-3587T>A

Variant names:

• chr7-105512131-A-T
• rs711432
• NM_019042.5:c.-32-3587T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_019042.5(PUS7):​c.-32-3587T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: PUS7 NM_019042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 0 publications found

Genes affected

PUS7 (HGNC:26033): (pseudouridine synthase 7) Enables enzyme binding activity and pseudouridine synthase activity. Involved in several processes, including pseudouridine synthesis; regulation of hematopoietic stem cell differentiation; and regulation of mesoderm development. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PUS7 Gene-Disease associations (from GenCC):

• intellectual developmental disorder with abnormal behavior, microcephaly, and short stature

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PUS7	NM_019042.5	c.-32-3587T>A		intron_variant	Intron 1 of 15	ENST00000469408.6	NP_061915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PUS7	ENST00000469408.6	c.-32-3587T>A		intron_variant	Intron 1 of 15	1	NM_019042.5	ENSP00000417402.1
PUS7	ENST00000356362.6	c.-8-3611T>A		intron_variant	Intron 1 of 15	2		ENSP00000348722.2
PUS7	ENST00000481939.5	n.-32-3587T>A		intron_variant	Intron 1 of 16	5		ENSP00000418794.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 131896 Hom.: 0 Cov.: 19

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

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 131896 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 63134

African (AFR) AF: 0.00 AC: 0 AN: 34494

American (AMR) AF: 0.00 AC: 0 AN: 12416

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3252

East Asian (EAS) AF: 0.00 AC: 0 AN: 4394

South Asian (SAS) AF: 0.00 AC: 0 AN: 3712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7914

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62882

Other (OTH) AF: 0.00 AC: 0 AN: 1722

Alfa AF: 0.00 Hom.: 799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.14
PhyloP100		-2.0

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

Other links and lift over

dbSNP: rs711432; hg19: chr7-105152578;