Genetic Variant NM_022900.5:c.7G>A (chr7-94510091-G-A) – 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_022900.5(CASD1):c.7G>A(p.Ala3Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000292 in 1,370,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000029 ( 0 hom. )

Consequence

CASD1
NM_022900.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.72

Publications

0 publications found

Variant links:

Genes affected

CASD1 (HGNC:16014): (CAS1 domain containing 1) Enables N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity. Involved in carbohydrate metabolic process. Is integral component of Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

CASD1 links:

ENSG00000309657 (HGNC:):

ENSG00000309657 links:

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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=0.13589644).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022900.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CASD1	NM_022900.5	MANE Select	c.7G>A	p.Ala3Thr	missense	Exon 1 of 18	NP_075051.4
CASD1	NM_001363426.1		c.-616G>A		5_prime_UTR	Exon 1 of 19	NP_001350355.1
CASD1	NM_001363428.1		c.-565G>A		5_prime_UTR	Exon 1 of 18	NP_001350357.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CASD1	ENST00000297273.9	TSL:1 MANE Select	c.7G>A	p.Ala3Thr	missense	Exon 1 of 18	ENSP00000297273.4	Q96PB1
CASD1	ENST00000919855.1		c.7G>A	p.Ala3Thr	missense	Exon 1 of 18	ENSP00000589914.1
CASD1	ENST00000919856.1		c.7G>A	p.Ala3Thr	missense	Exon 1 of 17	ENSP00000589915.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000740

AC:

AN:

135104

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000465

Gnomad ASJ 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:

0.00000292

AC:

AN:

1370754

Hom.:

Cov.:

AF XY:

0.00000296

AC XY:

AN XY:

675964

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

28952

American (AMR)

AF:

0.0000608

AC:

AN:

32908

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24364

East Asian (EAS)

AF:

0.00

AC:

AN:

33232

South Asian (SAS)

AF:

0.00

AC:

AN:

76212

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49016

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4130

European-Non Finnish (NFE)

AF:

0.00000188

AC:

AN:

1065356

Other (OTH)

AF:

0.00

AC:

AN:

56584

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

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.:

Alfa

AF:

0.00

Hom.:

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

-0.21

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.022

Eigen

Benign

-0.15

Eigen_PC

Benign

-0.032

FATHMM_MKL

Benign

0.19

LIST_S2

Uncertain

0.92

M_CAP

Pathogenic

0.41

MetaRNN

Benign

0.14

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.55

PhyloP100

3.7

PrimateAI

Pathogenic

0.83

PROVEAN

Benign

-0.50

REVEL

Benign

0.056

Sift

Benign

0.047

Sift4G

Benign

0.096

Polyphen

0.28

Vest4

0.12

MutPred

0.32

Loss of helix (P = 0.028)

MVP

0.31

MPC

0.40

ClinPred

0.28

GERP RS

3.5

PromoterAI

-0.22

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.12

gMVP

0.43

Mutation Taster

=82/18

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