chr17-45254648-A-G

Variant names:

• chr17-45254648-A-G
• rs8065345
• NM_152343.3:c.1068-135T>C

Variant summary

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

The NM_152343.3(SPATA32):​c.1068-135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 694,272 control chromosomes in the GnomAD database, including 14,687 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 0.25 (6993 hom., cov: 31)
  • Exomes 𝑓: 0.15 (7694 hom.)
• Consequence: SPATA32 NM_152343.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.12
• Publications: 8 publications found

Genes affected

SPATA32 (HGNC:26349): (spermatogenesis associated 32) Predicted to enable actin binding activity. Predicted to be involved in spermatogenesis. Predicted to be active in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MAP3K14-AS1 (HGNC:44359): (MAP3K14 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA32	NM_152343.3	c.1068-135T>C		intron_variant	Intron 4 of 4	ENST00000331780.5	NP_689556.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA32	ENST00000331780.5	c.1068-135T>C		intron_variant	Intron 4 of 4	1	NM_152343.3	ENSP00000331532.4

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38235 AN: 151786 Hom.: 6970 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.148 AC: 80116 AN: 542368 Hom.: 7694 AF XY: 0.143 AC XY: 41350 AN XY: 290100

African (AFR) AF: 0.510 AC: 7225 AN: 14170

American (AMR) AF: 0.173 AC: 4143 AN: 24008

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 1858 AN: 15606

East Asian (EAS) AF: 0.0214 AC: 698 AN: 32626

South Asian (SAS) AF: 0.0741 AC: 4064 AN: 54820

European-Finnish (FIN) AF: 0.175 AC: 6926 AN: 39516

Middle Eastern (MID) AF: 0.155 AC: 343 AN: 2214

European-Non Finnish (NFE) AF: 0.151 AC: 49857 AN: 330372

Other (OTH) AF: 0.172 AC: 5002 AN: 29036

GnomAD4 genome AF: 0.252 AC: 38302 AN: 151904 Hom.: 6993 Cov.: 31 AF XY: 0.247 AC XY: 18373 AN XY: 74252

African (AFR) AF: 0.514 AC: 21277 AN: 41392

American (AMR) AF: 0.191 AC: 2920 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3468

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5166

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4820

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10693 AN: 67910

Other (OTH) AF: 0.234 AC: 493 AN: 2106

Alfa AF: 0.184 Hom.: 12783

Bravo AF: 0.265

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.025
DANN	Benign	0.42
PhyloP100		-4.1
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: rs8065345; hg19: chr17-43332015;