rs4661748

Variant names:

• chr1-16413540-G-T
• rs4661748
• NM_198546.1:c.145-3497C>A

Variant summary

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

The NM_198546.1(SPATA21):​c.145-3497C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,070 control chromosomes in the GnomAD database, including 7,116 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 0.30 (7116 hom., cov: 32)
• Consequence: SPATA21 NM_198546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA21	NM_198546.1	c.145-3497C>A		intron_variant	Intron 5 of 12	ENST00000335496.5	NP_940948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA21	ENST00000335496.5	c.145-3497C>A		intron_variant	Intron 5 of 12	1	NM_198546.1	ENSP00000335612.1
SPATA21	ENST00000540400.1	c.-63-2625C>A		intron_variant	Intron 2 of 10	1		ENSP00000440046.1
SPATA21	ENST00000466212.5	n.1091-2625C>A		intron_variant	Intron 5 of 16	2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45670 AN: 151952 Hom.: 7108 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.301 AC: 45705 AN: 152070 Hom.: 7116 Cov.: 32 AF XY: 0.296 AC XY: 21981 AN XY: 74350

African (AFR) AF: 0.311 AC: 12899 AN: 41482

American (AMR) AF: 0.227 AC: 3459 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.173 AC: 898 AN: 5184

South Asian (SAS) AF: 0.167 AC: 805 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3338 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22434 AN: 67982

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.321 Hom.: 1149

Bravo AF: 0.295

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.0
DANN	Benign	0.87
PhyloP100		0.42
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: rs4661748; hg19: chr1-16740035; COSMIC: COSV59185964;