Genetic Variant NM_001008218.2:c.982C>G (chr1-103691507-G-C) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001008218.2(AMY1B):c.982C>G(p.Leu328Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L328I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 1)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AMY1B
NM_001008218.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.24

Publications

1 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.37943286).

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.982C>G	p.Leu328Val	missense	Exon 7 of 11	NP_001008219.1	P0DTE7
	AMY1B	NM_001386925.1		c.982C>G	p.Leu328Val	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.982C>G	p.Leu328Val	missense	Exon 7 of 11	ENSP00000330484.5	P0DTE7
AMY1B	ENST00000370080.7	TSL:2	c.982C>G	p.Leu328Val	missense	Exon 7 of 11	ENSP00000359097.3	P0DTE7
AMY1B	ENST00000903269.1		c.982C>G	p.Leu328Val	missense	Exon 7 of 11	ENSP00000573328.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

789090

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

393152

African (AFR)

AF:

0.00

AC:

AN:

9600

American (AMR)

AF:

0.00

AC:

AN:

27762

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12404

East Asian (EAS)

AF:

0.00

AC:

AN:

31358

South Asian (SAS)

AF:

0.00

AC:

AN:

47108

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33030

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2468

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

593304

Other (OTH)

AF:

0.00

AC:

AN:

32056

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000263

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

0.0097

BayesDel_noAF

Benign

-0.22

CADD

Benign

(source)

DANN

Benign

0.97

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.24

FATHMM_MKL

Uncertain

0.80

LIST_S2

Uncertain

0.92

M_CAP

Benign

0.077

MetaRNN

Benign

0.38

MetaSVM

Pathogenic

0.90

PhyloP100

2.2

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

-2.1

REVEL

Uncertain

0.42

Sift

Benign

0.067

Sift4G

Benign

0.24

Vest4

0.31

MutPred

0.82

Gain of MoRF binding (P = 0.1131)

MVP

0.20

ClinPred

0.79

GERP RS

2.1

gMVP

0.20

Mutation Taster

=93/7

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over