X-49332772-C-G

Position:

• chrX-49332772-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_001098412.4(GAGE13):​c.35C>G​(p.Pro12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 4)
  • Exomes 𝑓: 0.0000052 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: GAGE13 NM_001098412.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

Genes affected

GAGE13 (HGNC:29081): (G antigen 13)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08435115).
• BP6: Variant X-49332772-C-G is Benign according to our data. Variant chrX-49332772-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3280466.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAGE13	NM_001098412.4	c.35C>G	p.Pro12Arg	missense_variant	2/5	ENST00000612958.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAGE13	ENST00000612958.2	c.35C>G	p.Pro12Arg	missense_variant	2/5	1	NM_001098412.4	P1

Frequencies

GnomAD3 genomes Cov.: 4

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000521 AC: 3 AN: 575871 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 150663

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000255

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000463

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.57
DEOGEN2	Benign	0.027	T
FATHMM_MKL	Benign	0.0031	N
LIST_S2	Benign	0.36	T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-0.94	T
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.46	T
Sift4G	Benign	0.46	T
Vest4		0.17
MVP		0.072
ClinPred		0.031	T
GERP RS		-0.18
Varity_R		0.13
gMVP		0.013

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-49198750;