NM_001012970.3:c.56+5156G>C

Variant names:

• chr1-244369912-G-C
• rs3101457
• NM_001012970.3:c.56+5156G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001012970.3(SPMIP3):​c.56+5156G>C variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SPMIP3 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 10 publications found

Genes affected

SPMIP3 (HGNC:30435): (sperm microtubule inner protein 3)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012970.3. 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
	SPMIP3	NM_001012970.3	MANE Select	c.56+5156G>C		intron	N/A	NP_001012988.1
	SPMIP3	NM_001276348.2		c.56+5156G>C		intron	N/A	NP_001263277.1
	SPMIP3	NM_001276349.2		c.56+5156G>C		intron	N/A	NP_001263278.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPMIP3	ENST00000308105.5	TSL:2 MANE Select	c.56+5156G>C		intron	N/A	ENSP00000311218.4
	SPMIP3	ENST00000366537.5	TSL:1	c.56+5156G>C		intron	N/A	ENSP00000355495.1
	SPMIP3	ENST00000486803.1	TSL:2	n.155+5156G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.23
PhyloP100		-1.1

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: rs3101457; hg19: chr1-244533214;