8-7848765-C-A

Variant names:

• chr8-7848765-C-A
• NM_001395484.1:c.136C>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001395484.1(SPAG11A):​c.136C>A​(p.Gln46Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 10)
  • Exomes 𝑓: 0.0000011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPAG11A NM_001395484.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.39
• 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: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.35624337).

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.136C>A	p.Gln46Lys	missense	Exon 2 of 3	NP_001382413.1	A0A2R8Y853
	SPAG11A	NM_001081552.3		c.136C>A	p.Gln46Lys	missense	Exon 2 of 4	NP_001075021.2
	SPAG11A	NM_001363726.3		c.136C>A	p.Gln46Lys	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.136C>A	p.Gln46Lys	missense	Exon 2 of 3	ENSP00000496500.1	A0A2R8Y853
	SPAG11A	ENST00000400125.6	TSL:1	c.136C>A	p.Gln46Lys	missense	Exon 2 of 3	ENSP00000382990.2
	SPAG11A	ENST00000326558.9	TSL:1	c.136C>A	p.Gln46Lys	missense	Exon 2 of 4	ENSP00000316012.5	A0A0A0MR37

Frequencies

GnomAD3 genomes Cov.: 10

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000111 AC: 1 AN: 903944 Hom.: 0 Cov.: 12 AF XY: 0.00000219 AC XY: 1 AN XY: 455880

African (AFR) AF: 0.00 AC: 0 AN: 26272

American (AMR) AF: 0.00 AC: 0 AN: 29218

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18050

East Asian (EAS) AF: 0.00 AC: 0 AN: 31952

South Asian (SAS) AF: 0.00 AC: 0 AN: 61808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43698

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2962

European-Non Finnish (NFE) AF: 0.00000154 AC: 1 AN: 649152

Other (OTH) AF: 0.00 AC: 0 AN: 40832

GnomAD4 genome Cov.: 10

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	0.089
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.84
Eigen	Benign	-0.50
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.052	N
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.0060	T
MetaRNN	Benign	0.36	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.7	L
PhyloP100		2.4
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-2.2	N
REVEL	Benign	0.10
Sift	Benign	0.036	D
Sift4G	Benign	0.074	T
Vest4		0.23
MutPred		0.75		Gain of ubiquitination at Q46 (P = 0.0146)
MVP		0.16
MPC		2.9
ClinPred		0.15	T
GERP RS		1.7
gMVP		0.056
Mutation Taster		=96/4	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

hg19: chr8-7706287;