13-112424334-T-C

Variant names:

• chr13-112424334-T-C
• rs4907702
• NM_145248.5:c.446-8110T>C

Variant summary

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

The NM_145248.5(SPACA7):​c.446-8110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,034 control chromosomes in the GnomAD database, including 33,097 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 0.65 (33097 hom., cov: 32)
• Consequence: SPACA7 NM_145248.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 2 publications found

Genes affected

SPACA7 (HGNC:29575): (sperm acrosome associated 7) Predicted to act upstream of or within negative regulation of cell adhesion and single fertilization. Located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000295796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPACA7	NM_145248.5	c.446-8110T>C		intron_variant	Intron 5 of 6	ENST00000283550.8	NP_660291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPACA7	ENST00000283550.8	c.446-8110T>C		intron_variant	Intron 5 of 6	1	NM_145248.5	ENSP00000283550.3
SPACA7	ENST00000375699.3	c.353-8110T>C		intron_variant	Intron 4 of 5	3		ENSP00000364851.3
ENSG00000295796	ENST00000732758.1	n.224-32940A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99441 AN: 151916 Hom.: 33054 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.655 AC: 99535 AN: 152034 Hom.: 33097 Cov.: 32 AF XY: 0.655 AC XY: 48670 AN XY: 74294

African (AFR) AF: 0.768 AC: 31898 AN: 41512

American (AMR) AF: 0.605 AC: 9248 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1987 AN: 3472

East Asian (EAS) AF: 0.647 AC: 3310 AN: 5118

South Asian (SAS) AF: 0.701 AC: 3372 AN: 4808

European-Finnish (FIN) AF: 0.616 AC: 6515 AN: 10568

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41106 AN: 67960

Other (OTH) AF: 0.618 AC: 1307 AN: 2114

Alfa AF: 0.623 Hom.: 10375

Bravo AF: 0.655

Asia WGS AF: 0.645 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.91
DANN	Benign	0.47
PhyloP100		-2.2
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: rs4907702; hg19: chr13-113078648;