NM_001350978.3:c.323A>T

Variant names:

• chr9-88132969-T-A
• NM_001350978.3:c.323A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001350978.3(SPATA31C2):​c.323A>T​(p.Gln108Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 16)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31C2 NM_001350978.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.239
• Publications: 0 publications found

Genes affected

SPATA31C2 (HGNC:24508): (SPATA31 subfamily C member 2) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000307536 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350978.3. 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
	SPATA31C2	NM_001350978.3	MANE Select	c.323A>T	p.Gln108Leu	missense	Exon 3 of 4	NP_001337907.1	A0A8I5KWQ5
	SPATA31C2	NM_001166137.1		c.323A>T	p.Gln108Leu	missense	Exon 3 of 4	NP_001159609.1	B4DYI2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31C2	ENST00000324915.6	TSL:6 MANE Select	c.323A>T	p.Gln108Leu	missense	Exon 3 of 4	ENSP00000509734.1	A0A8I5KWQ5
	SPATA31C2	ENST00000675441.1		c.323A>T	p.Gln108Leu	missense	Exon 3 of 4	ENSP00000509164.1	B4DYI2
	ENSG00000307536	ENST00000826920.1		n.154+13136T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1238770 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 617942

African (AFR) AF: 0.00 AC: 0 AN: 24078

American (AMR) AF: 0.00 AC: 0 AN: 30274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21962

East Asian (EAS) AF: 0.00 AC: 0 AN: 28476

South Asian (SAS) AF: 0.00 AC: 0 AN: 73806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44666

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3444

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 961458

Other (OTH) AF: 0.00 AC: 0 AN: 50606

GnomAD4 genome Cov.: 16

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_noAF	Benign	-0.92
CADD	Benign	17
DANN	Benign	0.86
PhyloP100		-0.24

Splicing

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

Other links and lift over

hg19: chr9-90747884;