rs5945372

Positions:

• chrX-153400456-A-C
• chrX-153400456-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001367770.1(PNMA6E):​c.-72+788T>G 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 0.66 (17128 hom., 21363 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: PNMA6E NM_001367770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

Genes affected

PNMA6E (HGNC:50767): (PNMA family member 6E)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PNMA6E	NM_001367770.1	c.-72+788T>G		intron_variant		ENST00000445091.3	NP_001354699.1
PNMA6E	NM_001351293.2	c.-72+788T>G		intron_variant			NP_001338222.1
PNMA6E	NM_001351294.2	c.-72+214T>G		intron_variant			NP_001338223.1
PNMA6E	XM_047442374.1	c.-71-1536T>G		intron_variant			XP_047298330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNMA6E	ENST00000445091.3	c.-72+788T>G		intron_variant		2	NM_001367770.1	ENSP00000488500	P1
PNMA6E	ENST00000633844.1	c.-72+788T>G		intron_variant		3		ENSP00000488404

Frequencies

GnomAD3 genomes AF: 0.661 AC: 72652 AN: 109855 Hom.: 17128 Cov.: 23 AF XY: 0.659 AC XY: 21328 AN XY: 32355

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.617

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: InbreedingCoeff AF: 0.661 AC: 72682 AN: 109901 Hom.: 17128 Cov.: 23 AF XY: 0.659 AC XY: 21363 AN XY: 32411

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.623

Alfa AF: 0.612 Hom.: 10008

Bravo AF: 0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.34

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

Other links and lift over

dbSNP: rs5945372; hg19: chrX-152665914;