chr8-7848831-C-T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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. 11/19 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

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG11A	NM_001395484.1	c.202C>T	p.Pro68Ser	missense_variant	Exon 2 of 3	ENST00000642566.2	NP_001382413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG11A	ENST00000642566.2	c.202C>T	p.Pro68Ser	missense_variant	Exon 2 of 3		NM_001395484.1	ENSP00000496500.1

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

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 12

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 22, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.202C>T (p.P68S) alteration is located in exon 2 (coding exon 2) of the SPAG11A gene. This alteration results from a C to T substitution at nucleotide position 202, causing the proline (P) at amino acid position 68 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
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;.;T;.;T
M_CAP	Benign	0.051	D
MetaRNN	Uncertain	0.45	T;T;T;T;T
MetaSVM	Benign	-0.68	T
MutationAssessor	Benign	1.8	.;.;.;.;L
PrimateAI	Benign	0.44	T
PROVEAN	Pathogenic	-7.9	D;D;.;D;D
REVEL	Benign	0.24
Sift	Pathogenic	0.0	D;D;.;D;D
Sift4G	Pathogenic	0.0	D;D;.;D;D
Vest4		0.59
MutPred		0.62		Loss of catalytic residue at P68 (P = 0.0057);Loss of catalytic residue at P68 (P = 0.0057);Loss of catalytic residue at P68 (P = 0.0057);Loss of catalytic residue at P68 (P = 0.0057);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

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: chr8-7706353;