rs5906771

Variant names:

• chrX-49305467-C-A
• rs5906771
• NM_001098413.4:c.145C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-49305467-C-A
• chrX-49305467-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001098413.4(GAGE10):​c.145C>A​(p.Arg49Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 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. R49C) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., 2 hem., cov: 29)
  • Exomes 𝑓: 0.00025 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: GAGE10 NM_001098413.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 1 publications found

Genes affected

GAGE10 (HGNC:30968): (G antigen 10)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.003481716).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098413.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAGE10	NM_001098413.4	MANE Select	c.145C>A	p.Arg49Ser	missense	Exon 3 of 5	NP_001091883.3	A6NGK3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAGE10	ENST00000407599.4	TSL:5 MANE Select	c.145C>A	p.Arg49Ser	missense	Exon 3 of 5	ENSP00000385415.3	A6NGK3

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 254 AN: 110055 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00847

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000668

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000674

GnomAD2 exomes AF: 0.00125 AC: 121 AN: 97056 AF XY: 0.000383

Gnomad AFR exome AF: 0.0136

Gnomad AMR exome AF: 0.000795

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000228

Gnomad OTH exome AF: 0.000731

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000251 AC: 270 AN: 1074541 Hom.: 0 Cov.: 32 AF XY: 0.00000285 AC XY: 1 AN XY: 351083

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00854 AC: 216 AN: 25284

American (AMR) AF: 0.000563 AC: 19 AN: 33766

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19126

East Asian (EAS) AF: 0.00 AC: 0 AN: 29926

South Asian (SAS) AF: 0.0000188 AC: 1 AN: 53108

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29255

Middle Eastern (MID) AF: 0.000703 AC: 2 AN: 2844

European-Non Finnish (NFE) AF: 0.00000479 AC: 4 AN: 835785

Other (OTH) AF: 0.000616 AC: 28 AN: 45447

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00231 AC: 254 AN: 110102 Hom.: 0 Cov.: 29 AF XY: 0.0000614 AC XY: 2 AN XY: 32564

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00846 AC: 246 AN: 29095

American (AMR) AF: 0.000667 AC: 7 AN: 10487

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2640

East Asian (EAS) AF: 0.00 AC: 0 AN: 3551

South Asian (SAS) AF: 0.00 AC: 0 AN: 2739

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6097

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53088

Other (OTH) AF: 0.000665 AC: 1 AN: 1503

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000145 Hom.: 1

ExAC AF: 0.00105 AC: 113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.44
FATHMM_MKL	Benign	0.00028	N
MetaRNN	Benign	0.0035	T
MetaSVM	Benign	-1.0	T
PhyloP100		-0.50
PrimateAI	Benign	0.38	T
PROVEAN	Benign	3.1	N
REVEL	Benign	0.015
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Vest4		0.047
MutPred		0.26		Gain of phosphorylation at R49 (P = 0.0087)
MVP		0.048
MPC		0.0077
ClinPred		0.0047	T
GERP RS		-2.4
gMVP		0.015

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: rs5906771; hg19: chrX-49161946;