17-50548467-C-T

Variant names:

• chr17-50548467-C-T
• rs8076470
• NM_022827.4:c.296+14C>T

Variant summary

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

The NM_022827.4(SPATA20):​c.296+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,613,004 control chromosomes in the GnomAD database, including 132,672 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 0.48 (20518 hom., cov: 32)
  • Exomes 𝑓: 0.38 (112154 hom.)
• Consequence: SPATA20 NM_022827.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 32 publications found

Genes affected

SPATA20 (HGNC:26125): (spermatogenesis associated 20) Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Predicted to be located in extracellular region. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA20	NM_022827.4	c.296+14C>T		intron_variant	Intron 3 of 16	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2	c.248+14C>T		intron_variant	Intron 2 of 15		NP_001245301.1
SPATA20	NM_001258373.2	c.116+14C>T		intron_variant	Intron 3 of 16		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11	c.296+14C>T		intron_variant	Intron 3 of 16	1	NM_022827.4	ENSP00000006658.6

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73308 AN: 151948 Hom.: 20468 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.456

GnomAD2 exomes AF: 0.385 AC: 95925 AN: 249324 AF XY: 0.370

Gnomad AFR exome AF: 0.784

Gnomad AMR exome AF: 0.453

Gnomad ASJ exome AF: 0.490

Gnomad EAS exome AF: 0.116

Gnomad FIN exome AF: 0.359

Gnomad NFE exome AF: 0.386

Gnomad OTH exome AF: 0.391

GnomAD4 exome AF: 0.381 AC: 556726 AN: 1460938 Hom.: 112154 Cov.: 50 AF XY: 0.375 AC XY: 272749 AN XY: 726730

African (AFR) AF: 0.796 AC: 26636 AN: 33474

American (AMR) AF: 0.449 AC: 20031 AN: 44588

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 12630 AN: 26084

East Asian (EAS) AF: 0.113 AC: 4487 AN: 39696

South Asian (SAS) AF: 0.242 AC: 20885 AN: 86216

European-Finnish (FIN) AF: 0.365 AC: 19449 AN: 53288

Middle Eastern (MID) AF: 0.405 AC: 2334 AN: 5760

European-Non Finnish (NFE) AF: 0.383 AC: 426145 AN: 1111474

Other (OTH) AF: 0.400 AC: 24129 AN: 60358

GnomAD4 genome AF: 0.483 AC: 73419 AN: 152066 Hom.: 20518 Cov.: 32 AF XY: 0.475 AC XY: 35319 AN XY: 74316

African (AFR) AF: 0.777 AC: 32223 AN: 41476

American (AMR) AF: 0.456 AC: 6964 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3468

East Asian (EAS) AF: 0.125 AC: 645 AN: 5170

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4822

European-Finnish (FIN) AF: 0.348 AC: 3681 AN: 10586

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25567 AN: 67940

Other (OTH) AF: 0.463 AC: 977 AN: 2110

Alfa AF: 0.410 Hom.: 45146

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.43
PhyloP100		0.38
PromoterAI		0.029	Neutral
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: rs8076470; hg19: chr17-48625828; COSMIC: COSV50066997; COSMIC: COSV50066997;