NM_001166271.3:c.1654-5602C>T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000273167 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001166271.3	c.1654-5602C>T		intron_variant	Intron 2 of 12	ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2	c.1840-5602C>T		intron_variant	Intron 4 of 14		NP_001273721.1
SPATA13	NM_153023.4	c.-222-5602C>T		intron_variant	Intron 1 of 11		NP_694568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000382108.8	c.1654-5602C>T		intron_variant	Intron 2 of 12	5	NM_001166271.3	ENSP00000371542.3
ENSG00000273167	ENST00000382141.4	n.1654-7843C>T		intron_variant	Intron 4 of 15	5		ENSP00000371576.4

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

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.517

Alfa AF: 0.539 Hom.: 30320

Bravo AF: 0.512

Asia WGS AF: 0.650 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs1220597; hg19: chr13-24818013;