9-87923328-C-T

Position:

• chr9-87923328-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000706933.1(SPATA31C1):​c.3421C>T​(p.Gln1141Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. 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 0.0098 (11 hom., cov: 28)
  • Exomes 𝑓: 0.0034 (126 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31C1 ENST00000706933.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

Genes affected

SPATA31C1 (HGNC:27846): (SPATA31 subfamily C member 1) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC497256 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA31C1	NM_001145124.1	c.3421C>T	p.Gln1141Ter	stop_gained	4/4	ENST00000706933.1	NP_001138596.1
SPATA31C1	XM_011518702.1	c.3463C>T	p.Gln1155Ter	stop_gained	4/4		XP_011517004.1
LOC497256	NR_149022.1	n.472+9801G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA31C1	ENST00000706933.1	c.3421C>T	p.Gln1141Ter	stop_gained	4/4		NM_001145124.1	ENSP00000516655	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1456 AN: 148858 Hom.: 11 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.00369

Gnomad AMI AF: 0.0150

Gnomad AMR AF: 0.00927

Gnomad ASJ AF: 0.0111

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000629

Gnomad FIN AF: 0.00713

Gnomad MID AF: 0.0163

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.00876

GnomAD3 exomes AF: 0.00165 AC: 408 AN: 247644 Hom.: 11 AF XY: 0.00157 AC XY: 211 AN XY: 134664

Gnomad AFR exome AF: 0.000845

Gnomad AMR exome AF: 0.00218

Gnomad ASJ exome AF: 0.00210

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.000232

Gnomad NFE exome AF: 0.00235

Gnomad OTH exome AF: 0.00449

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00337 AC: 4853 AN: 1442034 Hom.: 126 Cov.: 33 AF XY: 0.00322 AC XY: 2312 AN XY: 717038

Gnomad4 AFR exome AF: 0.00115

Gnomad4 AMR exome AF: 0.00386

Gnomad4 ASJ exome AF: 0.00722

Gnomad4 EAS exome AF: 0.000102

Gnomad4 SAS exome AF: 0.000825

Gnomad4 FIN exome AF: 0.00421

Gnomad4 NFE exome AF: 0.00351

Gnomad4 OTH exome AF: 0.00504

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00977 AC: 1456 AN: 148976 Hom.: 11 Cov.: 28 AF XY: 0.00936 AC XY: 682 AN XY: 72840

Gnomad4 AFR AF: 0.00371

Gnomad4 AMR AF: 0.00926

Gnomad4 ASJ AF: 0.0111

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000420

Gnomad4 FIN AF: 0.00713

Gnomad4 NFE AF: 0.0154

Gnomad4 OTH AF: 0.00867

Alfa AF: 0.0151 Hom.: 9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Pathogenic	27
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs595203; hg19: chr9-90538243; COSMIC: COSV69665900;