8-7848831-C-T

Variant names:

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

Variant summary

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

The NM_001395484.1(SPAG11A):​c.202C>T​(p.Pro68Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 12)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPAG11A NM_001395484.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• 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>T	p.Pro68Ser	missense	Exon 2 of 3	NP_001382413.1	A0A2R8Y853
	SPAG11A	NM_001081552.3		c.202C>T	p.Pro68Ser	missense	Exon 2 of 4	NP_001075021.2
	SPAG11A	NM_001363726.3		c.202C>T	p.Pro68Ser	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>T	p.Pro68Ser	missense	Exon 2 of 3	ENSP00000496500.1	A0A2R8Y853
	SPAG11A	ENST00000400125.6	TSL:1	c.202C>T	p.Pro68Ser	missense	Exon 2 of 3	ENSP00000382990.2
	SPAG11A	ENST00000326558.9	TSL:1	c.202C>T	p.Pro68Ser	missense	Exon 2 of 4	ENSP00000316012.5	A0A0A0MR37

Frequencies

GnomAD3 genomes Cov.: 12

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 552938 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 287886

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: 0.00 AC: 0 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: 348692

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

GnomAD4 genome Cov.: 12

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Uncertain	0.072	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	18
DANN	Uncertain	1.0
Eigen	Benign	-0.13
Eigen_PC	Benign	-0.39
FATHMM_MKL	Benign	0.055	N
LIST_S2	Benign	0.79	T
M_CAP	Benign	0.051	D
MetaRNN	Uncertain	0.45	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	0.24
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.59
MutPred		0.62		Loss of catalytic residue at P68 (P = 0.0057)
MVP		0.17
MPC		3.3
ClinPred		0.96	D
GERP RS		2.1
gMVP		0.14
Mutation Taster		=89/11	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;