rs755435794

Variant names:

• chr1-13416419-C-G
• rs755435794
• NM_001099852.2:c.65C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-13416419-C-G
• chr1-13416419-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001099852.2(PRAMEF20):​c.65C>G​(p.Ala22Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 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. A22V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRAMEF20 NM_001099852.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 0 publications found

Genes affected

PRAMEF20 (HGNC:25224): (PRAME family member 20) Predicted to be involved in several processes, including negative regulation of apoptotic process; negative regulation of transcription, DNA-templated; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17957088).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRAMEF20	NM_001099852.2	c.65C>G	p.Ala22Gly	missense_variant	Exon 2 of 4	ENST00000602960.2	NP_001093322.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRAMEF20	ENST00000602960.2	c.65C>G	p.Ala22Gly	missense_variant	Exon 2 of 4	5	NM_001099852.2	ENSP00000473584.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Uncertain	0.98
DEOGEN2	Benign	0.15	T;T
Eigen	Benign	-0.57
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.0078	N
LIST_S2	Benign	0.21	T;.
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.18	T;T
MetaSVM	Benign	-1.0	T
PhyloP100		0.11
PrimateAI	Benign	0.45	T
PROVEAN	Uncertain	-3.2	D;.
REVEL	Benign	0.047
Sift	Benign	0.030	D;.
Sift4G	Benign	0.068	T;T
Vest4		0.21
MutPred		0.57		Loss of stability (P = 0.017);Loss of stability (P = 0.017);
MVP		0.014
ClinPred		0.33	T
GERP RS		-0.91
PromoterAI		-0.061	Neutral
Varity_R		0.033
gMVP		0.17
Mutation Taster		=99/1	polymorphism

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: rs755435794; hg19: chr1-13742876;