Genetic Variant NM_198475.3:c.1783G>A (chr17-44354431-C-T) – 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_198475.3(FAM171A2):c.1783G>A(p.Glu595Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000102 in 984,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 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: 0.0000010 ( 0 hom. )

Consequence

FAM171A2
NM_198475.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.02

Publications

0 publications found

Variant links:

Genes affected

FAM171A2 (HGNC:30480): (family with sequence similarity 171 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM171A2 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=0.097738415).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198475.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM171A2	NM_198475.3	MANE Select	c.1783G>A	p.Glu595Lys	missense	Exon 8 of 8	NP_940877.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM171A2	ENST00000293443.12	TSL:1 MANE Select	c.1783G>A	p.Glu595Lys	missense	Exon 8 of 8	ENSP00000293443.6	A8MVW0
FAM171A2	ENST00000912944.1		c.1819G>A	p.Glu607Lys	missense	Exon 9 of 9	ENSP00000583003.1
FAM171A2	ENST00000912945.1		c.1810G>A	p.Glu604Lys	missense	Exon 8 of 8	ENSP00000583004.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

5588

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR 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:

0.00000102

AC:

AN:

984954

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

467048

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18820

American (AMR)

AF:

0.00

AC:

AN:

4930

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9184

East Asian (EAS)

AF:

0.00

AC:

AN:

15942

South Asian (SAS)

AF:

0.0000527

AC:

AN:

18990

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23676

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2488

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

854978

Other (OTH)

AF:

0.00

AC:

AN:

35946

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

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.:

ExAC

AF:

0.000710

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

Benign

0.22

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0057

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.49

M_CAP

Uncertain

0.22

MetaRNN

Benign

0.098

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.69

PhyloP100

1.0

PrimateAI

Pathogenic

0.94

PROVEAN

Benign

-0.88

REVEL

Benign

0.035

Sift

Benign

0.20

Sift4G

Benign

0.59

Polyphen

0.88

Vest4

0.093

MutPred

0.41

Gain of glycosylation at E595 (P = 0.0054)

MVP

0.030

ClinPred

0.29

GERP RS

2.9

Varity_R

0.12

gMVP

0.23

Mutation Taster

=98/2

polymorphism

(source)

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

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