chr1-244376566-A-G

Variant names:

• chr1-244376566-A-G
• rs3102458
• NM_001012970.3:c.152+1099A>G

Variant summary

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

The NM_001012970.3(SPMIP3):​c.152+1099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,026 control chromosomes in the GnomAD database, including 3,509 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 0.21 (3509 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SPMIP3 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 2 publications found

Genes affected

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

ENSG00000240963 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPMIP3	NM_001012970.3	MANE Select	c.152+1099A>G		intron	N/A	NP_001012988.1
	SPMIP3	NM_001276348.2		c.152+1099A>G		intron	N/A	NP_001263277.1
	SPMIP3	NM_001276349.2		c.152+1099A>G		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.152+1099A>G		intron	N/A	ENSP00000311218.4
	SPMIP3	ENST00000366537.5	TSL:1	c.152+1099A>G		intron	N/A	ENSP00000355495.1
	ENSG00000240963	ENST00000417765.1	TSL:3	n.158-103T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32075 AN: 151908 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.211 AC: 32099 AN: 152026 Hom.: 3509 Cov.: 32 AF XY: 0.213 AC XY: 15848 AN XY: 74324

African (AFR) AF: 0.170 AC: 7050 AN: 41462

American (AMR) AF: 0.230 AC: 3516 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.185 AC: 954 AN: 5164

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4822

European-Finnish (FIN) AF: 0.241 AC: 2548 AN: 10562

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14912 AN: 67962

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.212 Hom.: 12202

Bravo AF: 0.207

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.61
PhyloP100		1.7
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: rs3102458; hg19: chr1-244539868;