Variant rs11096964 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_138389.4(FAM114A1):c.250G>A(p.Gly84Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,613,980 control chromosomes in the GnomAD database, including 59,769 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.27 ( 6118 hom., cov: 33)

Exomes 𝑓: 0.26 ( 53651 hom. )

Consequence

FAM114A1
NM_138389.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76

Variant links:

Genes affected

FAM114A1 (HGNC:25087): (family with sequence similarity 114 member A1) The protein encoded by this gene belongs to the FAM114 family and may play a role in neuronal cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

FAM114A1 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=0.0021304488).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM114A1	NM_138389.4 linkuse as main transcript	c.250G>A	p.Gly84Arg	missense_variant	3/15	ENST00000358869.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM114A1	ENST00000358869.5 linkuse as main transcript	c.250G>A	p.Gly84Arg	missense_variant	3/15	1	NM_138389.4	P1	Q8IWE2-1
FAM114A1	ENST00000510213.5 linkuse as main transcript	c.250G>A	p.Gly84Arg	missense_variant	2/3	2
FAM114A1	ENST00000515037.5 linkuse as main transcript	c.-274+10494G>A		intron_variant		2			Q8IWE2-2

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41710

AN:

152076

Hom.:

6096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.0842

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.228

GnomAD3 exomes

AF:

0.250

AC:

62350

AN:

249614

Hom.:

8645

AF XY:

0.241

AC XY:

32515

AN XY:

135160

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.274

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.0860

Gnomad SAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.359

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.265

AC:

387077

AN:

1461786

Hom.:

53651

Cov.:

AF XY:

0.261

AC XY:

189790

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.311

Gnomad4 AMR exome

AF:

0.264

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.0732

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.277

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.274

AC:

41773

AN:

152194

Hom.:

6118

Cov.:

AF XY:

0.271

AC XY:

20169

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.208

Gnomad4 ASJ

AF:

0.211

Gnomad4 EAS

AF:

0.0847

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.263

Hom.:

12204

Bravo

AF:

0.266

TwinsUK

AF:

0.269

AC:

999

ALSPAC

AF:

0.268

AC:

1033

ESP6500AA

AF:

0.313

AC:

1377

ESP6500EA

AF:

0.273

AC:

2352

ExAC

AF:

0.247

AC:

30048

Asia WGS

AF:

0.165

AC:

574

AN:

3478

EpiCase

AF:

0.265

EpiControl

AF:

0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

Cadd

Benign

Dann

Benign

0.97

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.61

LIST_S2

Benign

0.72

T;T

MetaRNN

Benign

0.0021

T;T

MetaSVM

Benign

-0.94

MutationTaster

Benign

0.95

P;P

PrimateAI

Benign

0.34

PROVEAN

Pathogenic

-7.0

D;N

REVEL

Benign

0.033

Sift

Benign

0.12

T;T

Sift4G

Uncertain

0.041

D;T

Polyphen

0.090

.;B

Vest4

0.038

MutPred

0.27

Gain of solvent accessibility (P = 0.0012);Gain of solvent accessibility (P = 0.0012);

MPC

0.083

ClinPred

0.018

GERP RS

1.9

Varity_R

0.040

gMVP

0.12

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