NM_001012970.3:c.325+2877G>A

Variant names:

• chr1-244381516-G-A
• rs3123710
• NM_001012970.3:c.325+2877G>A

Variant summary

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

The NM_001012970.3(SPMIP3):​c.325+2877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,096 control chromosomes in the GnomAD database, including 25,293 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 0.57 (25293 hom., cov: 33)
• Consequence: SPMIP3 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPMIP3	NM_001012970.3	c.325+2877G>A		intron_variant	Intron 4 of 4	ENST00000308105.5	NP_001012988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPMIP3	ENST00000308105.5	c.325+2877G>A		intron_variant	Intron 4 of 4	2	NM_001012970.3	ENSP00000311218.4

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86825 AN: 151978 Hom.: 25266 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.571 AC: 86900 AN: 152096 Hom.: 25293 Cov.: 33 AF XY: 0.569 AC XY: 42284 AN XY: 74342

African (AFR) AF: 0.596 AC: 24721 AN: 41462

American (AMR) AF: 0.570 AC: 8714 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2158 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1320 AN: 5176

South Asian (SAS) AF: 0.659 AC: 3178 AN: 4824

European-Finnish (FIN) AF: 0.555 AC: 5868 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39046 AN: 67984

Other (OTH) AF: 0.535 AC: 1131 AN: 2114

Alfa AF: 0.569 Hom.: 52228

Bravo AF: 0.567

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.41
PhyloP100		-2.1
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: rs3123710; hg19: chr1-244544818;