rs3860876

Variant names:

• chr8-7860744-A-C
• rs3860876
• NM_001395484.1:c.313A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-7860744-A-C
• chr8-7860744-A-G
• chr8-7860744-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001395484.1(SPAG11A):​c.313A>C​(p.Ser105Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 19)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPAG11A NM_001395484.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 6 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.11958158).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG11A	NM_001395484.1	MANE Select	c.313A>C	p.Ser105Arg	missense	Exon 3 of 3	NP_001382413.1
	SPAG11A	NM_001363726.3		c.*77A>C		3_prime_UTR	Exon 4 of 4	NP_001350655.1
	SPAG11A	NM_001081552.3		c.292+21A>C		intron	N/A	NP_001075021.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG11A	ENST00000642566.2	MANE Select	c.313A>C	p.Ser105Arg	missense	Exon 3 of 3	ENSP00000496500.1
	SPAG11A	ENST00000434307.6	TSL:1	c.*77A>C		3_prime_UTR	Exon 4 of 4	ENSP00000416991.2
	SPAG11A	ENST00000326558.9	TSL:1	c.292+21A>C		intron	N/A	ENSP00000316012.5

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1271192 Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0 AN XY: 629410

African (AFR) AF: 0.00 AC: 0 AN: 31194

American (AMR) AF: 0.00 AC: 0 AN: 37928

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21558

East Asian (EAS) AF: 0.00 AC: 0 AN: 28626

South Asian (SAS) AF: 0.00 AC: 0 AN: 65560

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46426

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5148

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 982290

Other (OTH) AF: 0.00 AC: 0 AN: 52462

GnomAD4 genome Cov.: 19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	21
DANN	Uncertain	0.98
DEOGEN2	Benign	0.016	T
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.56
FATHMM_MKL	Benign	0.24	N
LIST_S2	Benign	0.43	T
M_CAP	Benign	0.035	D
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.0	T
PhyloP100		1.5
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.038
Sift	Uncertain	0.0030	D
Sift4G	Uncertain	0.0040	D
Vest4		0.29
MutPred		0.47		Loss of phosphorylation at S52 (P = 0.0237)
MVP		0.072
ClinPred		0.18	T
GERP RS		2.3
Mutation Taster		=97/3	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3860876; hg19: chr8-7718266;