Variant rs3814165 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001010924.2(FAM171A1):c.1393C>T(p.Pro465Ser) variant causes a missense change. The variant allele was found at a frequency of 0.162 in 1,613,990 control chromosomes in the GnomAD database, including 22,353 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 0.13 ( 1619 hom., cov: 32)

Exomes 𝑓: 0.17 ( 20734 hom. )

Consequence

FAM171A1
NM_001010924.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.18

Variant links:

Genes affected

FAM171A1 (HGNC:23522): (family with sequence similarity 171 member A1) Involved in regulation of cell shape and stress fiber assembly. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM171A1 links:

LOC105376433 (HGNC:):

LOC105376433 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=0.0017546415).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM171A1	NM_001010924.2 linkuse as main transcript	c.1393C>T	p.Pro465Ser	missense_variant	8/8	ENST00000378116.9
LOC105376433	XR_007062068.1 linkuse as main transcript	n.85+5524G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM171A1	ENST00000378116.9 linkuse as main transcript	c.1393C>T	p.Pro465Ser	missense_variant	8/8	1	NM_001010924.2	P1
FAM171A1	ENST00000477161.1 linkuse as main transcript	n.593C>T		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19627

AN:

152020

Hom.:

1620

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0350

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.162

GnomAD3 exomes

AF:

0.151

AC:

37885

AN:

251392

Hom.:

3111

AF XY:

0.157

AC XY:

21381

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.0337

Gnomad AMR exome

AF:

0.0862

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.168

Gnomad SAS exome

AF:

0.173

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.165

AC:

241731

AN:

1461852

Hom.:

20734

Cov.:

AF XY:

0.166

AC XY:

121012

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0275

Gnomad4 AMR exome

AF:

0.0922

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.172

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.129

AC:

19627

AN:

152138

Hom.:

1619

Cov.:

AF XY:

0.130

AC XY:

9669

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.0349

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.169

Hom.:

5743

Bravo

AF:

0.124

TwinsUK

AF:

0.173

AC:

643

ALSPAC

AF:

0.168

AC:

648

ESP6500AA

AF:

0.0422

AC:

186

ESP6500EA

AF:

0.175

AC:

1504

ExAC

AF:

0.150

AC:

18171

Asia WGS

AF:

0.159

AC:

551

AN:

3478

EpiCase

AF:

0.182

EpiControl

AF:

0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.027

Eigen

Uncertain

0.29

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.71

MetaRNN

Benign

0.0018

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.3

MutationTaster

Benign

0.000056

PrimateAI

Benign

0.46

PROVEAN

Benign

-0.98

REVEL

Benign

0.080

Sift

Benign

0.22

Sift4G

Benign

0.53

Polyphen

0.89

Vest4

0.14

MPC

0.70

ClinPred

0.030

GERP RS

4.3

Varity_R

0.083

gMVP

0.28

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