chr1-12941141-C-A

Variant names:

• chr1-12941141-C-A
• rs761497343
• NM_001010889.2:c.712G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001010889.2(PRAMEF6):​c.712G>T​(p.Val238Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V238I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 2)
• Consequence: PRAMEF6 NM_001010889.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88

Genes affected

PRAMEF6 (HGNC:30583): (PRAME family member 6) Enables ubiquitin ligase-substrate adaptor activity. Involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.10060507).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRAMEF6	NM_001010889.2	c.712G>T	p.Val238Phe	missense_variant	Exon 3 of 4	ENST00000376189.5	NP_001010889.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRAMEF6	ENST00000376189.5	c.712G>T	p.Val238Phe	missense_variant	Exon 3 of 4	1	NM_001010889.2	ENSP00000365360.1
PRAMEF6	ENST00000415464.6	c.712G>T	p.Val238Phe	missense_variant	Exon 3 of 4	1		ENSP00000401281.2

Frequencies

GnomAD3 genomes Cov.: 2

GnomAD3 exomes AF: 0.0000196 AC: 1 AN: 51004 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 25654

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000135

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.042
DANN	Benign	0.31
DEOGEN2	Benign	0.0070	T;T
Eigen	Benign	-2.7
Eigen_PC	Benign	-2.8
FATHMM_MKL	Benign	0.00044	N
M_CAP	Benign	0.00069	T
MetaRNN	Benign	0.10	T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-0.18	N;N
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.59	N;N
REVEL	Benign	0.059
Sift	Benign	0.63	T;T
Sift4G	Benign	0.64	T;T
Polyphen		0.18	B;B
Vest4		0.099
MutPred		0.38		Loss of catalytic residue at V238 (P = 0.049);Loss of catalytic residue at V238 (P = 0.049);
MVP		0.043
MPC		2.1
ClinPred		0.036	T
GERP RS		-3.1
Varity_R		0.049
gMVP		0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs761497343; hg19: chr1-13000971;