rs17419150

Positions:

• chr1-16404087-C-G
• chr1-16404087-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198546.1(SPATA21):​c.812-48G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 1,502,446 control chromosomes in the GnomAD database, including 120,018 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 0.34 (10054 hom., cov: 31)
  • Exomes 𝑓: 0.40 (109964 hom.)
• Consequence: SPATA21 NM_198546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

SPATA21 (HGNC:28026): (spermatogenesis associated 21) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA21	NM_198546.1	c.812-48G>C		intron_variant		ENST00000335496.5	NP_940948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA21	ENST00000335496.5	c.812-48G>C		intron_variant		1	NM_198546.1	ENSP00000335612	P2
SPATA21	ENST00000540400.1	c.743-48G>C		intron_variant		1		ENSP00000440046	A2
SPATA21	ENST00000466212.5	n.2104-48G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51538 AN: 151880 Hom.: 10062 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.353

GnomAD3 exomes AF: 0.407 AC: 63643 AN: 156306 Hom.: 14098 AF XY: 0.411 AC XY: 33746 AN XY: 82040

Gnomad AFR exome AF: 0.139

Gnomad AMR exome AF: 0.357

Gnomad ASJ exome AF: 0.361

Gnomad EAS exome AF: 0.692

Gnomad SAS exome AF: 0.397

Gnomad FIN exome AF: 0.524

Gnomad NFE exome AF: 0.395

Gnomad OTH exome AF: 0.391

GnomAD4 exome AF: 0.396 AC: 534407 AN: 1350448 Hom.: 109964 Cov.: 22 AF XY: 0.397 AC XY: 265314 AN XY: 669122

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.358

Gnomad4 EAS exome AF: 0.699

Gnomad4 SAS exome AF: 0.397

Gnomad4 FIN exome AF: 0.520

Gnomad4 NFE exome AF: 0.390

Gnomad4 OTH exome AF: 0.395

GnomAD4 genome AF: 0.339 AC: 51531 AN: 151998 Hom.: 10054 Cov.: 31 AF XY: 0.347 AC XY: 25795 AN XY: 74286

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.350

Alfa AF: 0.368 Hom.: 2033

Bravo AF: 0.320

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.53

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: rs17419150; hg19: chr1-16730582; COSMIC: COSV59185815; COSMIC: COSV59185815;