rs4658635

Variant names:

• chr1-244366101-A-G
• rs4658635
• NM_001012970.3:c.56+1345A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-244366101-A-G
• chr1-244366101-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012970.3(SPMIP3):​c.56+1345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,042 control chromosomes in the GnomAD database, including 46,898 homozygotes. 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: 𝑓 0.78 (46898 hom., cov: 31)
• Consequence: SPMIP3 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPMIP3	NM_001012970.3	MANE Select	c.56+1345A>G		intron	N/A	NP_001012988.1
	SPMIP3	NM_001276348.2		c.56+1345A>G		intron	N/A	NP_001263277.1
	SPMIP3	NM_001276349.2		c.56+1345A>G		intron	N/A	NP_001263278.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPMIP3	ENST00000308105.5	TSL:2 MANE Select	c.56+1345A>G		intron	N/A	ENSP00000311218.4
	SPMIP3	ENST00000366537.5	TSL:1	c.56+1345A>G		intron	N/A	ENSP00000355495.1
	SPMIP3	ENST00000486803.1	TSL:2	n.155+1345A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119103 AN: 151924 Hom.: 46855 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.784 AC: 119205 AN: 152042 Hom.: 46898 Cov.: 31 AF XY: 0.790 AC XY: 58675 AN XY: 74296

African (AFR) AF: 0.789 AC: 32729 AN: 41464

American (AMR) AF: 0.833 AC: 12723 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4775 AN: 5174

South Asian (SAS) AF: 0.831 AC: 4004 AN: 4820

European-Finnish (FIN) AF: 0.798 AC: 8430 AN: 10566

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51766 AN: 67970

Other (OTH) AF: 0.800 AC: 1693 AN: 2116

Alfa AF: 0.761 Hom.: 36519

Bravo AF: 0.787

Asia WGS AF: 0.892 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.087
Mutation Taster		=100/0	polymorphism (auto)

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: rs4658635; hg19: chr1-244529403;