rs2270558

Positions:

• chr5-35654609-C-G
• chr5-35654609-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024867.4(SPEF2):​c.861C>G​(p.Asp287Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D287D) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SPEF2 NM_024867.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

SPEF2 (HGNC:26293): (sperm flagellar 2) Involved in sperm axoneme assembly. Located in sperm flagellum. Implicated in spermatogenic failure 43. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.087482244).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPEF2	NM_024867.4	c.861C>G	p.Asp287Glu	missense_variant	7/37	ENST00000356031.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPEF2	ENST00000356031.8	c.861C>G	p.Asp287Glu	missense_variant	7/37	1	NM_024867.4	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 43

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.023	.;.;T;T;.;.
Eigen	Benign	-0.69
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.73	T;T;T;T;T;T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.087	T;T;T;T;T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.9	L;.;.;L;.;L
MutationTaster	Benign	0.98	P;P;P;P
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-2.1	N;N;.;N;N;N
REVEL	Benign	0.10
Sift	Benign	0.25	T;T;.;T;T;T
Sift4G	Benign	0.43	T;T;.;T;D;T
Polyphen		0.44	B;P;.;D;.;.
Vest4		0.092
MutPred		0.16		Gain of phosphorylation at Y284 (P = 0.1025);Gain of phosphorylation at Y284 (P = 0.1025);Gain of phosphorylation at Y284 (P = 0.1025);Gain of phosphorylation at Y284 (P = 0.1025);.;Gain of phosphorylation at Y284 (P = 0.1025);
MVP		0.076
MPC		0.23
ClinPred		0.80	D
GERP RS		-3.9
Varity_R		0.065
gMVP		0.13

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

LitVar

Other links and lift over

dbSNP: rs2270558; hg19: chr5-35654711;