dbSNP rs654128: FAM162B:p.Gln71His (chr6-116765215-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001085480.3(FAM162B):c.213G>T(p.Gln71His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 1,613,708 control chromosomes in the GnomAD database, including 16,764 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1368 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15396 hom. )

Consequence

FAM162B
NM_001085480.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

Publications

39 publications found

Variant links:

Genes affected

FAM162B (HGNC:21549): (family with sequence similarity 162 member B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM162B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001049012).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM162B	NM_001085480.3 link	c.213G>T	p.Gln71His	missense_variant	Exon 2 of 4	ENST00000368557.6	NP_001078949.1	Q5T6X4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM162B	ENST00000368557.6 link	c.213G>T	p.Gln71His	missense_variant	Exon 2 of 4	1	NM_001085480.3	ENSP00000357545.4		Q5T6X4

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19115

AN:

152026

Hom.:

1371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0931

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.0571

Gnomad SAS

AF:

0.0371

Gnomad FIN

AF:

0.0982

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.158

GnomAD2 exomes

AF:

0.119

AC:

29757

AN:

249242

AF XY:

0.120

show subpopulations

Gnomad AFR exome

AF:

0.0916

Gnomad AMR exome

AF:

0.0906

Gnomad ASJ exome

AF:

0.276

Gnomad EAS exome

AF:

0.0481

Gnomad FIN exome

AF:

0.0932

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.140

AC:

204018

AN:

1461564

Hom.:

15396

Cov.:

AF XY:

0.138

AC XY:

100415

AN XY:

727108

show subpopulations

African (AFR)

AF:

0.0957

AC:

3203

AN:

33476

American (AMR)

AF:

0.0955

AC:

4271

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

7143

AN:

26118

East Asian (EAS)

AF:

0.0536

AC:

2127

AN:

39692

South Asian (SAS)

AF:

0.0427

AC:

3685

AN:

86254

European-Finnish (FIN)

AF:

0.0933

AC:

4970

AN:

53248

Middle Eastern (MID)

AF:

0.234

AC:

1348

AN:

5768

European-Non Finnish (NFE)

AF:

0.151

AC:

168093

AN:

1111902

Other (OTH)

AF:

0.152

AC:

9178

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

9672

19344

29017

38689

48361

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5880

11760

17640

23520

29400

<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

AF:

0.126

AC:

19106

AN:

152144

Hom.:

1368

Cov.:

AF XY:

0.122

AC XY:

9042

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0928

AC:

3855

AN:

41530

American (AMR)

AF:

0.131

AC:

2009

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.282

AC:

976

AN:

3462

East Asian (EAS)

AF:

0.0572

AC:

295

AN:

5154

South Asian (SAS)

AF:

0.0367

AC:

177

AN:

4824

European-Finnish (FIN)

AF:

0.0982

AC:

1041

AN:

10602

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10287

AN:

67966

Other (OTH)

AF:

0.156

AC:

330

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

856

1713

2569

3426

4282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.149

Hom.:

7741

Bravo

AF:

0.129

TwinsUK

AF:

0.136

AC:

505

ALSPAC

AF:

0.147

AC:

565

ESP6500AA

AF:

0.0939

AC:

407

ESP6500EA

AF:

0.158

AC:

1354

ExAC

AF:

0.117

AC:

14172

Asia WGS

AF:

0.0610

AC:

215

AN:

3478

EpiCase

AF:

0.172

EpiControl

AF:

0.171

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.66

CADD

Benign

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.0075

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.035

LIST_S2

Benign

0.65

MetaRNN

Benign

0.0010

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

PhyloP100

-2.0

PrimateAI

Benign

0.35

PROVEAN

Benign

-1.5

REVEL

Benign

0.12

Sift

Benign

0.081

Sift4G

Benign

0.18

Polyphen

0.97

Vest4

0.086

MutPred

0.12

Loss of MoRF binding (P = 0.1028);

MPC

1.2

ClinPred

0.068

GERP RS

-7.3

Varity_R

0.43

gMVP

0.41

Mutation Taster

=91/9

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over