X-153400456-A-C

Variant names:

• chrX-153400456-A-C
• rs5945372
• NM_001367770.1:c.-72+788T>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367770.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNMA6E	NM_001367770.1	MANE Select	c.-72+788T>G		intron	N/A	NP_001354699.1	A0A0J9YXQ4
	PNMA6E	NM_001351293.2		c.-72+788T>G		intron	N/A	NP_001338222.1	A0A0J9YXH5
	PNMA6E	NM_001351294.2		c.-72+214T>G		intron	N/A	NP_001338223.1	A0A0J9YXH5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNMA6E	ENST00000445091.3	TSL:2 MANE Select	c.-72+788T>G		intron	N/A	ENSP00000488500.1	A0A0J9YXQ4
	PNMA6E	ENST00000633844.1	TSL:3	c.-72+788T>G		intron	N/A	ENSP00000488404.1	A0A0J9YXH5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 72652 AN: 109855 Hom.: 17128 Cov.: 23

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

African (AFR) AF: 0.691 AC: 20828 AN: 30146

American (AMR) AF: 0.615 AC: 6491 AN: 10562

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 1592 AN: 2610

East Asian (EAS) AF: 0.655 AC: 2217 AN: 3387

South Asian (SAS) AF: 0.507 AC: 1316 AN: 2596

European-Finnish (FIN) AF: 0.687 AC: 4057 AN: 5906

Middle Eastern (MID) AF: 0.556 AC: 115 AN: 207

European-Non Finnish (NFE) AF: 0.664 AC: 34733 AN: 52330

Other (OTH) AF: 0.623 AC: 933 AN: 1498

Alfa AF: 0.626 Hom.: 14014

Bravo AF: 0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.34
PhyloP100		-2.4

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: rs5945372; hg19: chrX-152665914;