9-61191465-C-T

Variant names:

• chr9-61191465-C-T
• rs374438064
• NM_015667.2:c.202C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_015667.2(SPATA31A7):​c.202C>T​(p.Arg68Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,272,846 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R68Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00018 (6 hom., cov: 17)
  • Exomes 𝑓: 0.00013 (46 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA31A7 NM_015667.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.690
• Publications: 0 publications found

Genes affected

SPATA31A7 (HGNC:32007): (SPATA31 subfamily A member 7) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000304786 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.09756231).
• BS2: High Homozygotes in GnomAdExome4 at 46 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015667.2. 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
	SPATA31A7	NM_015667.2	MANE Select	c.202C>T	p.Arg68Trp	missense	Exon 2 of 4	NP_056482.2	Q8IWB4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31A7	ENST00000619167.2	TSL:1 MANE Select	c.202C>T	p.Arg68Trp	missense	Exon 2 of 4	ENSP00000484807.1	Q8IWB4
	SPATA31A7	ENST00000619140.4	TSL:5	n.138C>T		non_coding_transcript_exon	Exon 1 of 3
	SPATA31A7	ENST00000622751.4	TSL:4	n.53C>T		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.000181 AC: 21 AN: 116286 Hom.: 6 Cov.: 17

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000884

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000351

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000553 AC: 13 AN: 235194 AF XY: 0.0000391

Gnomad AFR exome AF: 0.000886

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000486

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000130 AC: 166 AN: 1272846 Hom.: 46 Cov.: 30 AF XY: 0.000160 AC XY: 101 AN XY: 631634

African (AFR) AF: 0.0000800 AC: 2 AN: 24986

American (AMR) AF: 0.0000528 AC: 2 AN: 37898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22454

East Asian (EAS) AF: 0.00 AC: 0 AN: 32118

South Asian (SAS) AF: 0.0000310 AC: 2 AN: 64566

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47870

Middle Eastern (MID) AF: 0.000502 AC: 2 AN: 3982

European-Non Finnish (NFE) AF: 0.000155 AC: 153 AN: 987368

Other (OTH) AF: 0.0000969 AC: 5 AN: 51604

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000181 AC: 21 AN: 116286 Hom.: 6 Cov.: 17 AF XY: 0.000160 AC XY: 9 AN XY: 56234

African (AFR) AF: 0.00 AC: 0 AN: 27762

American (AMR) AF: 0.0000884 AC: 1 AN: 11306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2858

East Asian (EAS) AF: 0.00 AC: 0 AN: 3276

South Asian (SAS) AF: 0.00 AC: 0 AN: 2812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8732

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 236

European-Non Finnish (NFE) AF: 0.000351 AC: 20 AN: 56980

Other (OTH) AF: 0.00 AC: 0 AN: 1578

Alfa AF: 0.0000843 Hom.: 0

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	-0.98
CADD	Benign	9.1
DANN	Benign	0.72
DEOGEN2	Benign	0.027	T
LIST_S2	Benign	0.50	T
MetaRNN	Benign	0.098	T
PhyloP100		-0.69
Sift4G	Benign	0.094	T
Vest4		0.22
gMVP		0.20

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: rs374438064; hg19: chr9-65508181;