Genetic Variant NM_015159.3:c.668A>G (chr11-73407571-T-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015159.3(FAM168A):c.668A>G(p.Gln223Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,455,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

FAM168A
NM_015159.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.94

Publications

0 publications found

Variant links:

Genes affected

FAM168A (HGNC:28999): (family with sequence similarity 168 member A) Involved in positive regulation of base-excision repair. [provided by Alliance of Genome Resources, Apr 2022]

FAM168A links:

ENSG00000256448 (HGNC:58441):

ENSG00000256448 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.25787047).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015159.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM168A	NM_015159.3	MANE Select	c.668A>G	p.Gln223Arg	missense	Exon 7 of 8	NP_055974.1	Q92567-2
FAM168A	NM_001286050.2		c.695A>G	p.Gln232Arg	missense	Exon 8 of 9	NP_001272979.1	Q92567-1
FAM168A	NM_001286051.2		c.350A>G	p.Gln117Arg	missense	Exon 5 of 6	NP_001272980.1	Q92567-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM168A	ENST00000356467.5	TSL:1 MANE Select	c.668A>G	p.Gln223Arg	missense	Exon 7 of 8	ENSP00000348852.4	Q92567-2
FAM168A	ENST00000064778.8	TSL:1	c.695A>G	p.Gln232Arg	missense	Exon 8 of 9	ENSP00000064778.4	Q92567-1
FAM168A	ENST00000450446.6	TSL:1	c.350A>G	p.Gln117Arg	missense	Exon 5 of 6	ENSP00000390501.2	Q92567-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000412

AC:

AN:

242574

AF XY:

0.00000758

show subpopulations

Gnomad AFR exome

AF:

0.0000667

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1455658

Hom.:

Cov.:

AF XY:

0.00000276

AC XY:

AN XY:

724220

show subpopulations

African (AFR)

AF:

0.0000303

AC:

AN:

32980

American (AMR)

AF:

0.00

AC:

AN:

43338

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25914

East Asian (EAS)

AF:

0.00

AC:

AN:

39014

South Asian (SAS)

AF:

0.00

AC:

AN:

85352

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53366

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5744

European-Non Finnish (NFE)

AF:

9.01e-7

AC:

AN:

1109822

Other (OTH)

AF:

0.00

AC:

AN:

60128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ESP6500AA

AF:

0.000243

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00000826

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.41

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Benign

-0.41

CADD

Pathogenic

(source)

DANN

Benign

0.76

DEOGEN2

Benign

0.083

Eigen

Benign

-0.50

Eigen_PC

Benign

-0.32

FATHMM_MKL

Uncertain

0.95

LIST_S2

Uncertain

0.87

M_CAP

Benign

0.0054

MetaRNN

Benign

0.26

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

PhyloP100

3.9

PrimateAI

Uncertain

0.71

PROVEAN

Benign

-1.7

REVEL

Benign

0.099

Sift

Benign

0.080

Sift4G

Benign

0.61

Polyphen

0.0

Vest4

0.70

MVP

0.12

MPC

1.1

ClinPred

0.25

GERP RS

2.0

Varity_R

0.20

gMVP

0.72

Mutation Taster

=77/23

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over