rs459920

Variant names:

• chr16-89664419-T-C
• rs459920
• NM_001271907.2:c.212-4867T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-89664419-T-C
• chr16-89664419-T-G

Variant summary

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

The NM_001271907.2(SPATA33):​c.212-4867T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,946 control chromosomes in the GnomAD database, including 10,699 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 0.35 (10699 hom., cov: 30)
• Consequence: SPATA33 NM_001271907.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 31 publications found

Genes affected

SPATA33 (HGNC:26463): (spermatogenesis associated 33) Predicted to act upstream of or within cellular protein localization; fertilization; and flagellated sperm motility. Predicted to be located in sperm mitochondrial sheath. Predicted to be active in cytoplasm and nucleus. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271907.2. 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
	SPATA33	NM_001271907.2	MANE Select	c.212-4867T>C		intron	N/A	NP_001258836.1	Q96N06-2
	SPATA33	NM_001387226.1		c.242-4867T>C		intron	N/A	NP_001374155.1
	SPATA33	NM_153025.3		c.209-4867T>C		intron	N/A	NP_694570.1	Q96N06-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA33	ENST00000579310.6	TSL:2 MANE Select	c.212-4867T>C		intron	N/A	ENSP00000462996.1	Q96N06-2
	SPATA33	ENST00000301031.8	TSL:1	c.209-4867T>C		intron	N/A	ENSP00000301031.4	Q96N06-1
	SPATA33	ENST00000566204.2	TSL:4	c.119-4867T>C		intron	N/A	ENSP00000461933.2	J3KRC8

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52995 AN: 151828 Hom.: 10696 Cov.: 30

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.349 AC: 53009 AN: 151946 Hom.: 10699 Cov.: 30 AF XY: 0.343 AC XY: 25486 AN XY: 74274

African (AFR) AF: 0.189 AC: 7811 AN: 41432

American (AMR) AF: 0.376 AC: 5742 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1908 AN: 3472

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4814

European-Finnish (FIN) AF: 0.387 AC: 4081 AN: 10540

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30615 AN: 67940

Other (OTH) AF: 0.427 AC: 901 AN: 2110

Alfa AF: 0.402 Hom.: 25151

Bravo AF: 0.343

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.68
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: rs459920; hg19: chr16-89730827;