rs767047424

Variant names:

• chr9-81945220-C-A
• rs767047424
• NM_207416.3:c.281C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-81945220-C-A
• chr9-81945220-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_207416.3(SPATA31D3):​c.281C>A​(p.Ser94Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00016 (0 hom., cov: 9)
  • Exomes 𝑓: 0.00015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31D3 NM_207416.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0550
• Publications: 1 publications found

Genes affected

SPATA31D3 (HGNC:38603): (SPATA31 subfamily D member 3) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267559 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.09050971).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207416.3. 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
	SPATA31D3	NM_207416.3	MANE Select	c.281C>A	p.Ser94Tyr	missense	Exon 3 of 4	NP_997299.2	P0C874
	LOC105376105	NR_188610.1		n.1039+1170G>T		intron	N/A
	LOC105376105	NR_188611.1		n.1228+981G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31D3	ENST00000445385.3	TSL:1 MANE Select	c.281C>A	p.Ser94Tyr	missense	Exon 3 of 4	ENSP00000488117.1	P0C874
	ENSG00000267559	ENST00000585776.5	TSL:2	n.1039+1170G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000158 AC: 9 AN: 56998 Hom.: 0 Cov.: 9

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000892

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00225

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000921

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000251 AC: 20 AN: 79756 AF XY: 0.000236

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00101

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000311

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000153 AC: 117 AN: 765844 Hom.: 0 Cov.: 15 AF XY: 0.000220 AC XY: 84 AN XY: 382156

⚠️ 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: 14836

American (AMR) AF: 0.00231 AC: 21 AN: 9088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9994

East Asian (EAS) AF: 0.00 AC: 0 AN: 9532

South Asian (SAS) AF: 0.00153 AC: 79 AN: 51510

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23324

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1776

European-Non Finnish (NFE) AF: 0.0000243 AC: 15 AN: 618546

Other (OTH) AF: 0.0000734 AC: 2 AN: 27238

⚠️ 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 Data not reliable, filtered out with message: AS_VQSR AF: 0.000158 AC: 9 AN: 57010 Hom.: 0 Cov.: 9 AF XY: 0.000234 AC XY: 6 AN XY: 25612

African (AFR) AF: 0.00 AC: 0 AN: 14088

American (AMR) AF: 0.000891 AC: 3 AN: 3366

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1888

East Asian (EAS) AF: 0.00 AC: 0 AN: 1900

South Asian (SAS) AF: 0.00226 AC: 3 AN: 1330

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 672

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 54

European-Non Finnish (NFE) AF: 0.0000921 AC: 3 AN: 32586

Other (OTH) AF: 0.00 AC: 0 AN: 704

Alfa AF: 0.0000617 Hom.: 0

ExAC AF: 0.000239 AC: 5

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	Benign	0.11
BayesDel_noAF	Benign	-0.92
CADD	Benign	17
DANN	Benign	0.46
DEOGEN2	Benign	0.14	T
FATHMM_MKL	Benign	0.0084	N
LIST_S2	Benign	0.69	T
MetaRNN	Benign	0.091	T
MutationAssessor	Uncertain	2.6	M
PhyloP100		-0.055
PrimateAI	Uncertain	0.49	T
Sift4G	Uncertain	0.0030	D
Polyphen		0.95	P
Vest4		0.35
GERP RS		-0.90
Varity_R		0.092
gMVP		0.050
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs767047424; hg19: chr9-84560135;