Variant 9-34724062-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001141917.2(SPATA31F1):c.3178C>T(p.His1060Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,166,718 control chromosomes in the GnomAD database, including 170,687 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 13177 hom., cov: 26)

Exomes 𝑓: 0.46 ( 157510 hom. )

Consequence

SPATA31F1
NM_001141917.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.63

Variant links:

Genes affected

SPATA31F1 (HGNC:41911): (SPATA31 subfamily F member 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31F1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.5235513E-5).

BP6

Variant 9-34724062-G-A is Benign according to our data. Variant chr9-34724062-G-A is described in ClinVar as [Benign]. Clinvar id is 402843.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SPATA31F1	NM_001141917.2 linkuse as main transcript	c.3178C>T	p.His1060Tyr	missense_variant	4/4	ENST00000378788.4	NP_001135389.1
PHF24	XM_047423102.1 linkuse as main transcript	c.133+21024G>A		intron_variant			XP_047279058.1
PHF24	XM_047423103.1 linkuse as main transcript	c.70+21024G>A		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA31F1	ENST00000378788.4 linkuse as main transcript	c.3178C>T	p.His1060Tyr	missense_variant	4/4	2	NM_001141917.2	ENSP00000417711	P1
	ENST00000664167.1 linkuse as main transcript	n.86+21024G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

57158

AN:

148460

Hom.:

13170

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.618

Gnomad SAS

AF:

0.518

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.386

GnomAD3 exomes

AF:

0.387

AC:

45115

AN:

116532

Hom.:

11907

AF XY:

0.384

AC XY:

22985

AN XY:

59884

show subpopulations

Gnomad AFR exome

AF:

0.0951

Gnomad AMR exome

AF:

0.412

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.595

Gnomad SAS exome

AF:

0.378

Gnomad FIN exome

AF:

0.413

Gnomad NFE exome

AF:

0.405

Gnomad OTH exome

AF:

0.369

GnomAD4 exome

AF:

0.458

AC:

466799

AN:

1018138

Hom.:

157510

Cov.:

AF XY:

0.458

AC XY:

232097

AN XY:

506440

show subpopulations

Gnomad4 AFR exome

AF:

0.0711

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.631

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.491

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.437

GnomAD4 genome

AF:

0.385

AC:

57183

AN:

148580

Hom.:

13177

Cov.:

AF XY:

0.387

AC XY:

28011

AN XY:

72324

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.416

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.618

Gnomad4 SAS

AF:

0.519

Gnomad4 FIN

AF:

0.500

Gnomad4 NFE

AF:

0.498

Gnomad4 OTH

AF:

0.392

Alfa

AF:

0.418

Hom.:

3102

Bravo

AF:

0.373

ExAC

AF:

0.290

AC:

7015

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.60

CADD

Benign

5.1

DANN

Benign

0.97

DEOGEN2

Benign

0.0049

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.068

LIST_S2

Benign

0.65

MetaRNN

Benign

0.000025

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

MutationTaster

Benign

1.0

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.59

REVEL

Benign

0.065

Sift

Benign

1.0

Sift4G

Uncertain

0.035

Polyphen

0.67

Vest4

0.040

ClinPred

0.011

GERP RS

3.2

Varity_R

0.025

gMVP

0.069

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