chr13-24243875-C-T

Variant names:

• chr13-24243875-C-T
• rs1220597
• NM_001166271.3:c.1654-5602C>T

Variant summary

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

The NM_001166271.3(SPATA13):​c.1654-5602C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,960 control chromosomes in the GnomAD database, including 20,615 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 0.52 (20615 hom., cov: 31)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 8 publications found

Genes affected

SPATA13 (HGNC:23222): (spermatogenesis associated 13) Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA13 Gene-Disease associations (from GenCC):

• primary angle-closure glaucoma

  Inheritance: AD Classification: MODERATE, LIMITED Submitted by: ClinGen, PanelApp Australia

ENSG00000273167 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166271.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	NM_001166271.3	MANE Select	c.1654-5602C>T		intron	N/A	NP_001159743.1	Q96N96-6
	SPATA13	NM_001286792.2		c.1840-5602C>T		intron	N/A	NP_001273721.1
	SPATA13	NM_153023.4		c.-222-5602C>T		intron	N/A	NP_694568.1	Q96N96-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	ENST00000382108.8	TSL:5 MANE Select	c.1654-5602C>T		intron	N/A	ENSP00000371542.3	Q96N96-6
	SPATA13	ENST00000424834.6	TSL:1	c.1654-5602C>T		intron	N/A	ENSP00000398560.2	Q96N96-6
	ENSG00000273167	ENST00000382141.4	TSL:5	n.1654-7843C>T		intron	N/A	ENSP00000371576.4	A0A0A0MRY4

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78657 AN: 151842 Hom.: 20608 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.518 AC: 78685 AN: 151960 Hom.: 20615 Cov.: 31 AF XY: 0.519 AC XY: 38553 AN XY: 74282

African (AFR) AF: 0.432 AC: 17910 AN: 41434

American (AMR) AF: 0.529 AC: 8074 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1864 AN: 3472

East Asian (EAS) AF: 0.708 AC: 3670 AN: 5182

South Asian (SAS) AF: 0.569 AC: 2737 AN: 4814

European-Finnish (FIN) AF: 0.559 AC: 5893 AN: 10544

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36890 AN: 67944

Other (OTH) AF: 0.517 AC: 1089 AN: 2108

Alfa AF: 0.536 Hom.: 41512

Bravo AF: 0.512

Asia WGS AF: 0.650 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.66
PhyloP100		-0.94
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: rs1220597; hg19: chr13-24818013;