12-48755814-A-G

Variant names:

• chr12-48755814-A-G
• rs953673
• NM_001351123.2:c.80-3395A>G

Variant summary

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

The NM_001351123.2(SPMIP11):​c.80-3395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,216 control chromosomes in the GnomAD database, including 10,417 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 0.35 (10417 hom., cov: 29)
• Consequence: SPMIP11 NM_001351123.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 3 publications found

Genes affected

SPMIP11 (HGNC:48628): (sperm microtubule inner protein 11)

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 (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPMIP11	NM_001351123.2	c.80-3395A>G		intron_variant	Intron 1 of 3	ENST00000548380.6	NP_001338052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPMIP11	ENST00000548380.6	c.80-3395A>G		intron_variant	Intron 1 of 3	1	NM_001351123.2	ENSP00000489652.1
SPMIP11	ENST00000548054.2	n.*24-3395A>G		intron_variant	Intron 2 of 4	1		ENSP00000490870.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53554 AN: 151110 Hom.: 10414 Cov.: 29

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.354 AC: 53579 AN: 151216 Hom.: 10417 Cov.: 29 AF XY: 0.342 AC XY: 25202 AN XY: 73750

African (AFR) AF: 0.279 AC: 11471 AN: 41178

American (AMR) AF: 0.280 AC: 4233 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1314 AN: 3460

East Asian (EAS) AF: 0.00618 AC: 32 AN: 5176

South Asian (SAS) AF: 0.207 AC: 997 AN: 4820

European-Finnish (FIN) AF: 0.357 AC: 3673 AN: 10276

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30611 AN: 67880

Other (OTH) AF: 0.328 AC: 689 AN: 2098

Alfa AF: 0.411 Hom.: 42424

Bravo AF: 0.346

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs953673; hg19: chr12-49149597;