9-34724062-G-A

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

2
16

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]
PHF24 (HGNC:29180): (PHD finger protein 24) Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. [provided by Alliance of Genome Resources, Apr 2022]

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 UniProt
SPATA31F1NM_001141917.2 linkuse as main transcriptc.3178C>T p.His1060Tyr missense_variant 4/4 ENST00000378788.4 NP_001135389.1
PHF24XM_047423102.1 linkuse as main transcriptc.133+21024G>A intron_variant XP_047279058.1
PHF24XM_047423103.1 linkuse as main transcriptc.70+21024G>A intron_variant XP_047279059.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM205AENST00000378788.4 linkuse as main transcriptc.3178C>T p.His1060Tyr missense_variant 4/42 NM_001141917.2 ENSP00000417711.1 Q6ZU69
ENSG00000288583ENST00000664167.1 linkuse as main transcriptn.86+21024G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
57158
AN:
148460
Hom.:
13170
Cov.:
26
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.:
41
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.:
26
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 submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant 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
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
5.1
DANN
Benign
0.97
DEOGEN2
Benign
0.0049
T
Eigen
Benign
-0.77
Eigen_PC
Benign
-0.85
FATHMM_MKL
Benign
0.068
N
LIST_S2
Benign
0.65
T
MetaRNN
Benign
0.000025
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.59
N
REVEL
Benign
0.065
Sift
Benign
1.0
T
Sift4G
Uncertain
0.035
D
Polyphen
0.67
P
Vest4
0.040
ClinPred
0.011
T
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.

Other links and lift over

dbSNP: rs472644; hg19: chr9-34724059; COSMIC: COSV66488496; API