Variant rs6007594 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_017911.4(FAM118A):c.716G>A(p.Arg239His) variant causes a missense change. The variant allele was found at a frequency of 0.308 in 1,613,870 control chromosomes in the GnomAD database, including 88,987 homozygotes. In-silico tool predicts 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 0.43 ( 17398 hom., cov: 32)

Exomes 𝑓: 0.30 ( 71589 hom. )

Consequence

FAM118A
NM_017911.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.95

Variant links:

Genes affected

FAM118A (HGNC:1313): (family with sequence similarity 118 member A) Enables identical protein binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM118A 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=5.4712627E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM118A	NM_017911.4 linkuse as main transcript	c.716G>A	p.Arg239His	missense_variant	6/9	ENST00000441876.7	NP_060381.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM118A	ENST00000441876.7 linkuse as main transcript	c.716G>A	p.Arg239His	missense_variant	6/9	1	NM_017911.4	ENSP00000395892	P1	Q9NWS6-1

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64878

AN:

151958

Hom.:

17362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.407

GnomAD3 exomes

AF:

0.353

AC:

88875

AN:

251440

Hom.:

18139

AF XY:

0.349

AC XY:

47374

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.761

Gnomad AMR exome

AF:

0.372

Gnomad ASJ exome

AF:

0.342

Gnomad EAS exome

AF:

0.484

Gnomad SAS exome

AF:

0.424

Gnomad FIN exome

AF:

0.237

Gnomad NFE exome

AF:

0.274

Gnomad OTH exome

AF:

0.343

GnomAD4 exome

AF:

0.296

AC:

432647

AN:

1461794

Hom.:

71589

Cov.:

AF XY:

0.298

AC XY:

216827

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.770

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.334

Gnomad4 EAS exome

AF:

0.465

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.238

Gnomad4 NFE exome

AF:

0.262

Gnomad4 OTH exome

AF:

0.338

GnomAD4 genome

AF:

0.427

AC:

64976

AN:

152076

Hom.:

17398

Cov.:

AF XY:

0.425

AC XY:

31584

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.752

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.429

Gnomad4 FIN

AF:

0.233

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.413

Alfa

AF:

0.307

Hom.:

19775

Bravo

AF:

0.452

TwinsUK

AF:

0.258

AC:

958

ALSPAC

AF:

0.261

AC:

1004

ESP6500AA

AF:

0.743

AC:

3274

ESP6500EA

AF:

0.271

AC:

2331

ExAC

AF:

0.360

AC:

43725

Asia WGS

AF:

0.504

AC:

1754

AN:

3478

EpiCase

AF:

0.285

EpiControl

AF:

0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.041

T;T

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.90

.;D

MetaRNN

Benign

0.0000055

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.0049

P;P;P

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.59

N;N

REVEL

Benign

0.11

Sift

Benign

0.19

T;T

Sift4G

Benign

0.17

T;T

Polyphen

1.0

D;D

Vest4

0.13

MPC

0.87

ClinPred

0.031

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.040

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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