NM_001395484.1:c.202C>G

Variant names:

• chr8-7848831-C-G
• rs1438569474
• NM_001395484.1:c.202C>G

Variant summary

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

The NM_001395484.1(SPAG11A):​c.202C>G​(p.Pro68Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. 14/21 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. P68S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 12)
  • Exomes 𝑓: 0.0000018 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPAG11A NM_001395484.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 0 publications found

Genes affected

SPAG11A (HGNC:33342): (sperm associated antigen 11A) Involved in antimicrobial humoral immune response mediated by antimicrobial peptide and cytolysis by host of symbiont cells. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC124901865 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395484.1. 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
	SPAG11A	NM_001395484.1	MANE Select	c.202C>G	p.Pro68Ala	missense	Exon 2 of 3	NP_001382413.1	A0A2R8Y853
	SPAG11A	NM_001081552.3		c.202C>G	p.Pro68Ala	missense	Exon 2 of 4	NP_001075021.2
	SPAG11A	NM_001363726.3		c.202C>G	p.Pro68Ala	missense	Exon 2 of 4	NP_001350655.1	J3KR45

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG11A	ENST00000642566.2	MANE Select	c.202C>G	p.Pro68Ala	missense	Exon 2 of 3	ENSP00000496500.1	A0A2R8Y853
	SPAG11A	ENST00000400125.6	TSL:1	c.202C>G	p.Pro68Ala	missense	Exon 2 of 3	ENSP00000382990.2
	SPAG11A	ENST00000326558.9	TSL:1	c.202C>G	p.Pro68Ala	missense	Exon 2 of 4	ENSP00000316012.5	A0A0A0MR37

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 98738 Hom.: 0 Cov.: 12

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00

GnomAD2 exomes AF: 0.0000169 AC: 1 AN: 59256 AF XY: 0.0000337

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000181 AC: 1 AN: 552940 Hom.: 0 Cov.: 6 AF XY: 0.00000347 AC XY: 1 AN XY: 287888

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

African (AFR) AF: 0.00 AC: 0 AN: 18898

American (AMR) AF: 0.00 AC: 0 AN: 23218

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14746

East Asian (EAS) AF: 0.00 AC: 0 AN: 30190

South Asian (SAS) AF: 0.0000199 AC: 1 AN: 50172

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2176

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 348694

Other (OTH) AF: 0.00 AC: 0 AN: 29260

⚠️ 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: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 98738 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 45752

African (AFR) AF: 0.00 AC: 0 AN: 28826

American (AMR) AF: 0.00 AC: 0 AN: 7968

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2526

East Asian (EAS) AF: 0.00 AC: 0 AN: 3430

South Asian (SAS) AF: 0.00 AC: 0 AN: 2374

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5830

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 45702

Other (OTH) AF: 0.00 AC: 0 AN: 1198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Uncertain	0.98
Eigen	Benign	-0.13
Eigen_PC	Benign	-0.39
FATHMM_MKL	Benign	0.070	N
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.048	D
MetaRNN	Uncertain	0.42	T
MetaSVM	Benign	-0.68	T
MutationAssessor	Benign	1.8	L
PhyloP100		2.5
PrimateAI	Benign	0.44	T
PROVEAN	Pathogenic	-7.9	D
REVEL	Benign	0.23
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.57
MutPred		0.63		Loss of glycosylation at P68 (P = 0.0093)
MVP		0.17
MPC		3.2
ClinPred		0.68	D
GERP RS		2.1
gMVP		0.063
Mutation Taster		=87/13	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: rs1438569474; hg19: chr8-7706353;