Variant 1-103691591-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000330330.10(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
ENST00000330330.10 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.74

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 made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMY1B	NM_001008218.2 linkuse as main transcript	c.898G>A	p.Gly300Ser	missense_variant	7/11	ENST00000330330.10	NP_001008219.1
AMY1B	NM_001386925.1 linkuse as main transcript	c.898G>A	p.Gly300Ser	missense_variant	7/11		NP_001373854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMY1B	ENST00000330330.10 linkuse as main transcript	c.898G>A	p.Gly300Ser	missense_variant	7/11	1	NM_001008218.2	ENSP00000330484	P1
AMY1B	ENST00000370080.7 linkuse as main transcript	c.898G>A	p.Gly300Ser	missense_variant	7/11	2		ENSP00000359097	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

24326

Hom.:

Cov.:

FAILED QC

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

GnomAD3 exomes

AF:

0.000145

AC:

AN:

82888

Hom.:

AF XY:

0.000244

AC XY:

AN XY:

45072

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 SAS 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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000854

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000195

Gnomad4 OTH exome

AF:

0.000284

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

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000735

Gnomad4 OTH

AF:

0.00

ExAC

AF:

0.000199

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 10, 2023

The c.898G>A (p.G300S) alteration is located in exon 7 (coding exon 6) of the AMY1B gene. This alteration results from a G to A substitution at nucleotide position 898, causing the glycine (G) at amino acid position 300 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.21

BayesDel_noAF

Uncertain

0.060

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Benign

0.011

Eigen_PC

Benign

-0.031

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.93

.;D

M_CAP

Uncertain

0.19

MetaRNN

Uncertain

0.48

T;T

MetaSVM

Pathogenic

1.0

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.61

PROVEAN

Pathogenic

-4.5

D;D

REVEL

Pathogenic

0.86

Sift

Benign

0.043

D;D

Sift4G

Uncertain

0.033

D;D

Vest4

0.37

MutPred

0.78

Gain of MoRF binding (P = 0.1304);Gain of MoRF binding (P = 0.1304);

MVP

0.31

ClinPred

0.65

GERP RS

2.1

gMVP

0.39

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over