Variant rs1919128 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032266.5(SPATA31H1):c.12532A>G(p.Ile4178Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,613,474 control chromosomes in the GnomAD database, including 63,845 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 5642 hom., cov: 32)

Exomes 𝑓: 0.27 ( 58203 hom. )

Consequence

SPATA31H1
NM_032266.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.28

Variant links:

Genes affected

SPATA31H1 (HGNC:25275): (SPATA31 subfamily H member 1) Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31H1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0011802316).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA31H1	NM_032266.5 linkuse as main transcript	c.12532A>G	p.Ile4178Val	missense_variant	5/5	ENST00000447166.3	NP_115642.4	Q68DN1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf16	ENST00000447166.3 linkuse as main transcript	c.12532A>G	p.Ile4178Val	missense_variant	5/5	3	NM_032266.5	ENSP00000403181.2		C9JG08

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36777

AN:

151968

Hom.:

5638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.296

GnomAD3 exomes

AF:

0.304

AC:

75801

AN:

249398

Hom.:

13582

AF XY:

0.293

AC XY:

39660

AN XY:

135310

show subpopulations

Gnomad AFR exome

AF:

0.0645

Gnomad AMR exome

AF:

0.522

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.478

Gnomad SAS exome

AF:

0.197

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.271

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.271

AC:

396218

AN:

1461386

Hom.:

58203

Cov.:

AF XY:

0.269

AC XY:

195813

AN XY:

727028

show subpopulations

Gnomad4 AFR exome

AF:

0.0618

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.338

Gnomad4 EAS exome

AF:

0.535

Gnomad4 SAS exome

AF:

0.200

Gnomad4 FIN exome

AF:

0.285

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.277

GnomAD4 genome

AF:

0.242

AC:

36790

AN:

152088

Hom.:

5642

Cov.:

AF XY:

0.249

AC XY:

18522

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0728

Gnomad4 AMR

AF:

0.436

Gnomad4 ASJ

AF:

0.339

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.272

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.275

Hom.:

10730

Bravo

AF:

0.249

TwinsUK

AF:

0.255

AC:

947

ALSPAC

AF:

0.255

AC:

981

ESP6500AA

AF:

0.0729

AC:

266

ESP6500EA

AF:

0.271

AC:

2207

ExAC

AF:

0.287

AC:

34624

Asia WGS

AF:

0.297

AC:

1035

AN:

3478

EpiCase

AF:

0.294

EpiControl

AF:

0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.00087

.;T

Eigen

Benign

-0.011

Eigen_PC

Benign

-0.079

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.50

T;T

MetaRNN

Benign

0.0012

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.97

.;L

PROVEAN

Benign

-0.41

.;N

REVEL

Benign

0.10

Sift

Pathogenic

0.0

.;D

Sift4G

Uncertain

0.016

.;D

Polyphen

0.97

.;D

Vest4

0.057

MPC

0.39

ClinPred

0.057

GERP RS

1.2

Varity_R

0.13

gMVP

0.056

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over