Genetic Variant SLC44A2:c.331-44A>G (chr19-10631231-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000335757.10(SLC44A2):c.331-44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,606,624 control chromosomes in the GnomAD database, including 492,213 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 48582 hom., cov: 29)

Exomes 𝑓: 0.78 ( 443631 hom. )

Consequence

SLC44A2
ENST00000335757.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.37

Publications

16 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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000335757.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC44A2	NM_020428.4	MANE Select	c.331-44A>G	intron	N/A	NP_065161.3
SLC44A2	NM_001363611.2		c.331-44A>G	intron	N/A	NP_001350540.1
SLC44A2	NM_001145056.2		c.325-44A>G	intron	N/A	NP_001138528.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC44A2	ENST00000335757.10	TSL:1 MANE Select	c.331-44A>G	intron	N/A	ENSP00000336888.4
SLC44A2	ENST00000407327.8	TSL:1	c.325-44A>G	intron	N/A	ENSP00000385135.3
SLC44A2	ENST00000588465.5	TSL:1	n.240-44A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.800

AC:

121199

AN:

151586

Hom.:

48555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.705

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.771

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.815

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.795

GnomAD2 exomes

AF:

0.793

AC:

199130

AN:

251258

AF XY:

0.786

show subpopulations

Gnomad AFR exome

AF:

0.834

Gnomad AMR exome

AF:

0.877

Gnomad ASJ exome

AF:

0.755

Gnomad EAS exome

AF:

0.689

Gnomad FIN exome

AF:

0.825

Gnomad NFE exome

AF:

0.785

Gnomad OTH exome

AF:

0.773

GnomAD4 exome

AF:

0.780

AC:

1134808

AN:

1454920

Hom.:

443631

Cov.:

AF XY:

0.779

AC XY:

564049

AN XY:

724204

show subpopulations

African (AFR)

AF:

0.834

AC:

27809

AN:

33328

American (AMR)

AF:

0.872

AC:

39007

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.756

AC:

19735

AN:

26104

East Asian (EAS)

AF:

0.664

AC:

26341

AN:

39650

South Asian (SAS)

AF:

0.760

AC:

65444

AN:

86096

European-Finnish (FIN)

AF:

0.824

AC:

44026

AN:

53412

Middle Eastern (MID)

AF:

0.694

AC:

3994

AN:

5756

European-Non Finnish (NFE)

AF:

0.780

AC:

861911

AN:

1105704

Other (OTH)

AF:

0.774

AC:

46541

AN:

60148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

12890

25780

38670

51560

64450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20434

40868

61302

81736

102170

<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

AF:

0.799

AC:

121276

AN:

151704

Hom.:

48582

Cov.:

AF XY:

0.799

AC XY:

59243

AN XY:

74106

show subpopulations

African (AFR)

AF:

0.836

AC:

34597

AN:

41380

American (AMR)

AF:

0.827

AC:

12536

AN:

15166

Ashkenazi Jewish (ASJ)

AF:

0.771

AC:

2673

AN:

3468

East Asian (EAS)

AF:

0.684

AC:

3493

AN:

5108

South Asian (SAS)

AF:

0.766

AC:

3686

AN:

4810

European-Finnish (FIN)

AF:

0.815

AC:

8581

AN:

10530

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.783

AC:

53193

AN:

67930

Other (OTH)

AF:

0.792

AC:

1670

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1235

2470

3706

4941

6176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<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:

0.791

Hom.:

9799

Bravo

AF:

0.799

Asia WGS

AF:

0.763

AC:

2655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.12

(source)

DANN

Benign

0.57

PhyloP100

-3.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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