Variant 2-27580222-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_032266.5(SPATA31H1):c.13862T>C(p.Leu4621Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,614,194 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 50 hom. )

Consequence

SPATA31H1
NM_032266.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.41

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003681302).

BP6

Variant 2-27580222-T-C is Benign according to our data. Variant chr2-27580222-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2650774.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA31H1	NM_032266.5 link	c.13862T>C	p.Leu4621Ser	missense_variant	Exon 5 of 5	ENST00000447166.3	NP_115642.4	Q68DN1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf16	ENST00000447166.3 link	c.13862T>C	p.Leu4621Ser	missense_variant	Exon 5 of 5	3	NM_032266.5	ENSP00000403181.2		C9JG08

Frequencies

GnomAD3 genomes

AF:

0.00501

AC:

762

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00497

Gnomad FIN

AF:

0.00405

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00672

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00541

AC:

1349

AN:

249470

Hom.:

AF XY:

0.00601

AC XY:

814

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.00168

Gnomad AMR exome

AF:

0.00261

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.00614

Gnomad FIN exome

AF:

0.00445

Gnomad NFE exome

AF:

0.00696

Gnomad OTH exome

AF:

0.00677

GnomAD4 exome

AF:

0.00596

AC:

8709

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00604

AC XY:

4395

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00246

Gnomad4 ASJ exome

AF:

0.0101

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00682

Gnomad4 FIN exome

AF:

0.00537

Gnomad4 NFE exome

AF:

0.00636

Gnomad4 OTH exome

AF:

0.00553

GnomAD4 genome

AF:

0.00501

AC:

763

AN:

152308

Hom.:

Cov.:

AF XY:

0.00474

AC XY:

353

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00518

Gnomad4 FIN

AF:

0.00405

Gnomad4 NFE

AF:

0.00672

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00565

Hom.:

Bravo

AF:

0.00477

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.00106

AC:

ESP6500EA

AF:

0.00583

AC:

ExAC

AF:

0.00581

AC:

702

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00523

EpiControl

AF:

0.00646

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SPATA31H1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.29

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.00090

.;T

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.51

FATHMM_MKL

Benign

0.49

LIST_S2

Benign

0.41

T;T

MetaRNN

Benign

0.0037

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.0

.;N

PROVEAN

Benign

-1.0

.;N

REVEL

Benign

0.041

Sift

Uncertain

0.0010

.;D

Sift4G

Uncertain

0.025

.;D

Polyphen

0.12

.;B

Vest4

0.16

MVP

0.055

MPC

0.15

ClinPred

0.048

GERP RS

4.0

Varity_R

0.15

gMVP

0.051

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over