9-81930129-G-T

Variant names:

• chr9-81930129-G-T
• rs1338446823
• NM_001145197.1:c.262G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001145197.1(SPATA31D4):​c.262G>T​(p.Glu88*) 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: not found (cov: 0)
  • Exomes 𝑓: 0.0000043 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31D4 NM_001145197.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 0 publications found

Genes affected

SPATA31D4 (HGNC:38601): (SPATA31 subfamily D member 4) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230846 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145197.1. 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
	SPATA31D4	NM_001145197.1	MANE Select	c.262G>T	p.Glu88*	stop_gained	Exon 3 of 4	NP_001138669.1	Q6ZUB0
	LOC105376105	NR_188610.1		n.1325+980C>A		intron	N/A
	LOC105376105	NR_188611.1		n.1514+980C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31D4	ENST00000419782.5	TSL:1 MANE Select	c.262G>T	p.Glu88*	stop_gained	Exon 3 of 4	ENSP00000488251.1	Q6ZUB0
	ENSG00000230846	ENST00000427387.1	TSL:3	n.260+980C>A		intron	N/A
	ENSG00000267559	ENST00000585776.5	TSL:2	n.*97C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000429 AC: 1 AN: 233186 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 125002

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 5470

American (AMR) AF: 0.00 AC: 0 AN: 5178

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5988

East Asian (EAS) AF: 0.00 AC: 0 AN: 2798

South Asian (SAS) AF: 0.00 AC: 0 AN: 25484

European-Finnish (FIN) AF: 0.0000970 AC: 1 AN: 10306

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 948

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 166072

Other (OTH) AF: 0.00 AC: 0 AN: 10942

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Pathogenic	26
DANN	Benign	0.67
FATHMM_MKL	Benign	0.015	N
PhyloP100		0.54
Vest4		0.031
GERP RS		0.66
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.20		Position offset: -29

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

Other links and lift over

dbSNP: rs1338446823; hg19: chr9-84545044;