rs3102458

Variant names:

• chr1-244376566-A-C
• NM_001012970.3:c.152+1099A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-244376566-A-C
• chr1-244376566-A-G
• chr1-244376566-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001012970.3(SPMIP3):​c.152+1099A>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: 32)
• Consequence: SPMIP3 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

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

ENSG00000240963 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPMIP3	NM_001012970.3	c.152+1099A>C		intron_variant	Intron 3 of 4	ENST00000308105.5	NP_001012988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf100	ENST00000308105.5	c.152+1099A>C		intron_variant	Intron 3 of 4	2	NM_001012970.3	ENSP00000311218.4
C1orf100	ENST00000366537.5	c.152+1099A>C		intron_variant	Intron 3 of 4	1		ENSP00000355495.1
ENSG00000240963	ENST00000417765.1	n.158-103T>G		intron_variant	Intron 2 of 3	3
C1orf100	ENST00000486803.1	n.251+1099A>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.62

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-244539868;