14-19424265-T-C

Position:

• chr14-19424265-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001005356.3(POTEG):​c.955A>G​(p.Ser319Gly) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 29)
• Consequence: POTEG NM_001005356.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

POTEG (HGNC:33896): (POTE ankyrin domain family member G)

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POTEG	NM_001005356.3	c.955A>G	p.Ser319Gly	missense_variant	5/11	ENST00000547848.5
LOC101929572	NR_110504.1	n.1763T>C		non_coding_transcript_exon_variant	2/2
POTEG	NR_027480.2	n.1007A>G		non_coding_transcript_exon_variant	5/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POTEG	ENST00000547848.5	c.955A>G	p.Ser319Gly	missense_variant	5/11	1	NM_001005356.3	P1
	ENST00000621705.1	n.1814T>C		non_coding_transcript_exon_variant	2/2	1
POTEG	ENST00000622767.4	c.955A>G	p.Ser319Gly	missense_variant, NMD_transcript_variant	5/12	1
POTEG	ENST00000547722.1	c.*242A>G		3_prime_UTR_variant, NMD_transcript_variant	6/12	2

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.89
DEOGEN2	Benign	0.0080	T
Eigen	Benign	-0.54
Eigen_PC	Benign	-0.80
FATHMM_MKL	Benign	0.0067	N
LIST_S2	Benign	0.55	T
M_CAP	Benign	0.0087	T
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-0.83	T
MutationTaster	Benign	1.0	N
PrimateAI	Pathogenic	0.81	D
PROVEAN	Benign	-1.6	N
Sift	Benign	0.15	T
Sift4G	Benign	0.20	T
Vest4		0.20
MutPred		0.53		Gain of catalytic residue at V321 (P = 0);
MVP		0.38
ClinPred		0.33	T
GERP RS		0.91
Varity_R		0.053
gMVP		0.035

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.53		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.53		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-20010203;