Genetic Variant AMY1B:p.Gly300Ser (chr1-103691591-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001008218.2(AMY1B):c.898G>A(p.Gly300Ser) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000041 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00015 ( 25 hom. )

Failed GnomAD Quality Control

Consequence

AMY1B
NM_001008218.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.74

Publications

0 publications found

Variant links:

Genes affected

AMY1B (HGNC:475): (amylase alpha 1B) Amylases are secreted proteins that hydrolyze 1,4-alpha-glucoside bonds in oligosaccharides and polysaccharides, and thus catalyze the first step in digestion of dietary starch and glycogen. The human genome has a cluster of several amylase genes that are expressed at high levels in either salivary gland or pancreas. This gene encodes an amylase isoenzyme produced by the salivary gland. [provided by RefSeq, Jul 2008]

AMY1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008218.2. 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
	AMY1B	NM_001008218.2	MANE Select	c.898G>A	p.Gly300Ser	missense	Exon 7 of 11	NP_001008219.1	P0DTE7
	AMY1B	NM_001386925.1		c.898G>A	p.Gly300Ser	missense	Exon 7 of 11	NP_001373854.1	P0DTE7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
AMY1B	ENST00000330330.10	TSL:1 MANE Select	c.898G>A	p.Gly300Ser	missense	Exon 7 of 11	ENSP00000330484.5	P0DTE7
AMY1B	ENST00000370080.7	TSL:2	c.898G>A	p.Gly300Ser	missense	Exon 7 of 11	ENSP00000359097.3	P0DTE7
AMY1B	ENST00000903269.1		c.898G>A	p.Gly300Ser	missense	Exon 7 of 11	ENSP00000573328.1

Frequencies

GnomAD3 genomes

AF:

0.0000411

AC:

AN:

24326

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000145

AC:

AN:

82888

AF XY:

0.000244

show subpopulations

Gnomad AFR exome

AF:

0.00

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:

0.000319

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000152

AC:

AN:

507832

Hom.:

Cov.:

AF XY:

0.000180

AC XY:

AN XY:

261148

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

5706

American (AMR)

AF:

0.0000854

AC:

AN:

23430

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8842

East Asian (EAS)

AF:

0.00

AC:

AN:

26718

South Asian (SAS)

AF:

0.00

AC:

AN:

38158

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28634

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1582

European-Non Finnish (NFE)

AF:

0.000195

AC:

AN:

353654

Other (OTH)

AF:

0.000284

AC:

AN:

21108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000411

AC:

AN:

24326

Hom.:

Cov.:

AF XY:

0.0000860

AC XY:

AN XY:

11632

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

3184

American (AMR)

AF:

0.00

AC:

AN:

2778

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

566

East Asian (EAS)

AF:

0.00

AC:

AN:

1386

South Asian (SAS)

AF:

0.00

AC:

AN:

520

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1712

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000735

AC:

AN:

13608

Other (OTH)

AF:

0.00

AC:

AN:

260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

ExAC

AF:

0.000199

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

0.13

BayesDel_addAF

Pathogenic

0.21

BayesDel_noAF

Uncertain

0.060

CADD

Uncertain

(source)

DANN

Uncertain

1.0

Eigen

Benign

0.011

Eigen_PC

Benign

-0.031

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.93

M_CAP

Uncertain

0.19

MetaRNN

Uncertain

0.48

MetaSVM

Pathogenic

1.0

PhyloP100

3.7

PrimateAI

Uncertain

0.61

PROVEAN

Pathogenic

-4.5

REVEL

Pathogenic

0.86

Sift

Benign

0.043

Sift4G

Uncertain

0.033

Vest4

0.37

MutPred

0.78

Gain of MoRF binding (P = 0.1304)

MVP

0.31

ClinPred

0.65

GERP RS

2.1

gMVP

0.39

Mutation Taster

=88/12

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over