chrX-153400456-A-T

Position:

• chrX-153400456-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367770.1(PNMA6E):​c.-72+788T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000908 in 110,096 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. 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 0.0000091 (0 hom., 1 hem., cov: 23)
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00000908 AC: 1 AN: 110096 Hom.: 0 Cov.: 23 AF XY: 0.0000307 AC XY: 1 AN XY: 32578

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000293

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 AF: 0.00000908 AC: 1 AN: 110096 Hom.: 0 Cov.: 23 AF XY: 0.0000307 AC XY: 1 AN XY: 32578

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000293

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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;