Genetic Variant NM_020428.4:c.11A>G (chr19-10625644-A-G) – 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_020428.4(SLC44A2):c.11A>G(p.Glu4Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC44A2
NM_020428.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.89

Publications

0 publications found

Variant links:

Genes affected

SLC44A2 (HGNC:17292): (solute carrier family 44 member 2 (CTL2 blood group)) Enables choline transmembrane transporter activity. Involved in choline transport and transmembrane transport. Located in mitochondrion and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC44A2 links:

Genome browser will be placed here

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=0.08900058).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020428.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC44A2	NM_020428.4	MANE Select	c.11A>G	p.Glu4Gly	missense	Exon 1 of 22	NP_065161.3
SLC44A2	NM_001363611.2		c.11A>G	p.Glu4Gly	missense	Exon 1 of 23	NP_001350540.1	Q8IWA5-2
SLC44A2	NM_001145056.2		c.32-609A>G		intron	N/A	NP_001138528.1	A0A088QCU6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC44A2	ENST00000335757.10	TSL:1 MANE Select	c.11A>G	p.Glu4Gly	missense	Exon 1 of 22	ENSP00000336888.4	Q8IWA5-1
SLC44A2	ENST00000407327.8	TSL:1	c.32-609A>G		intron	N/A	ENSP00000385135.3	Q8IWA5-3
SLC44A2	ENST00000588465.5	TSL:1	n.106-609A>G		intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1096770

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

519212

African (AFR)

AF:

0.00

AC:

AN:

23014

American (AMR)

AF:

0.00

AC:

AN:

8564

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14432

East Asian (EAS)

AF:

0.00

AC:

AN:

26580

South Asian (SAS)

AF:

0.00

AC:

AN:

21690

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31204

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4148

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

923106

Other (OTH)

AF:

0.00

AC:

AN:

44032

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

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

0.071

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.61

CADD

Uncertain

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.028

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.50

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.67

M_CAP

Benign

0.025

MetaRNN

Benign

0.089

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.90

PhyloP100

1.9

PrimateAI

Uncertain

0.52

PROVEAN

Benign

-1.0

REVEL

Benign

0.080

Sift

Benign

0.18

Sift4G

Benign

0.15

Polyphen

0.0

Vest4

0.16

MutPred

0.10

Loss of solvent accessibility (P = 0.0187)

MVP

0.38

MPC

0.40

ClinPred

0.14

GERP RS

4.1

PromoterAI

-0.090

Neutral

(source)

Varity_R

0.14

gMVP

0.64

Mutation Taster

=76/24

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over