9-42183738-C-T

Variant names:

• chr9-42183738-C-T
• rs746632976
• NM_001145196.1:c.51C>T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001145196.1(SPATA31A6):​c.51C>T​(p.Asn17Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,534,826 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00027 (3 hom., cov: 23)
  • Exomes 𝑓: 0.00042 (101 hom.)
• Consequence: SPATA31A6 NM_001145196.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.278

Genes affected

SPATA31A6 (HGNC:32006): (SPATA31 subfamily A member 6) Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 9-42183738-C-T is Benign according to our data. Variant chr9-42183738-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659218.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.278 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31A6	NM_001145196.1	c.51C>T	p.Asn17Asn	synonymous_variant	Exon 1 of 4	ENST00000332857.7	NP_001138668.1
SPATA31A6	XM_011517871.4	c.51C>T	p.Asn17Asn	synonymous_variant	Exon 1 of 4		XP_011516173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31A6	ENST00000332857.7	c.51C>T	p.Asn17Asn	synonymous_variant	Exon 1 of 4	1	NM_001145196.1	ENSP00000329825.6

Frequencies

GnomAD3 genomes AF: 0.000269 AC: 36 AN: 133648 Hom.: 3 Cov.: 23

Gnomad AFR AF: 0.000154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000448

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000247

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000315

Gnomad OTH AF: 0.00219

GnomAD4 exome AF: 0.000425 AC: 595 AN: 1401178 Hom.: 101 Cov.: 34 AF XY: 0.000409 AC XY: 285 AN XY: 697382

Gnomad4 AFR exome AF: 0.000136

Gnomad4 AMR exome AF: 0.000420

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000537

Gnomad4 SAS exome AF: 0.000444

Gnomad4 FIN exome AF: 0.0000829

Gnomad4 NFE exome AF: 0.000466

Gnomad4 OTH exome AF: 0.000521

GnomAD4 genome AF: 0.000269 AC: 36 AN: 133648 Hom.: 3 Cov.: 23 AF XY: 0.000216 AC XY: 14 AN XY: 64868

Gnomad4 AFR AF: 0.000154

Gnomad4 AMR AF: 0.000448

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000247

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000315

Gnomad4 OTH AF: 0.00219

Alfa AF: 0.000409 Hom.: 3

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SPATA31A6: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.2
DANN	Benign	0.90

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

Publications

LitVar

Other links and lift over

dbSNP: rs746632976; hg19: chr9-40700370;