dbSNP rs1560711: SLC44A2:c.503-15C>T (chr19-10631611-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020428.4(SLC44A2):c.503-15C>T 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 1,613,388 control chromosomes in the GnomAD database, including 494,889 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 ( 48879 hom., cov: 33)

Exomes 𝑓: 0.78 ( 446010 hom. )

Consequence

SLC44A2
NM_020428.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49

Publications

18 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:

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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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

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	Effect	Exon Rank	Protein	UniProt
SLC44A2	NM_020428.4	MANE Select	c.503-15C>T	intron	N/A	NP_065161.3
SLC44A2	NM_001363611.2		c.503-15C>T	intron	N/A	NP_001350540.1	Q8IWA5-2
SLC44A2	NM_001145056.2		c.497-15C>T	intron	N/A	NP_001138528.1	A0A088QCU6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC44A2	ENST00000335757.10	TSL:1 MANE Select	c.503-15C>T	intron	N/A	ENSP00000336888.4	Q8IWA5-1
SLC44A2	ENST00000407327.8	TSL:1	c.497-15C>T	intron	N/A	ENSP00000385135.3	Q8IWA5-3
SLC44A2	ENST00000588465.5	TSL:1	n.412-15C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121741

AN:

152032

Hom.:

48853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.841

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.769

Gnomad EAS

AF:

0.684

Gnomad SAS

AF:

0.773

Gnomad FIN

AF:

0.813

Gnomad MID

AF:

0.704

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.796

GnomAD2 exomes

AF:

0.793

AC:

198074

AN:

249860

AF XY:

0.786

show subpopulations

Gnomad AFR exome

AF:

0.839

Gnomad AMR exome

AF:

0.876

Gnomad ASJ exome

AF:

0.754

Gnomad EAS exome

AF:

0.687

Gnomad FIN exome

AF:

0.824

Gnomad NFE exome

AF:

0.784

Gnomad OTH exome

AF:

0.774

GnomAD4 exome

AF:

0.780

AC:

1140364

AN:

1461238

Hom.:

446010

Cov.:

AF XY:

0.779

AC XY:

566514

AN XY:

726898

show subpopulations

African (AFR)

AF:

0.839

AC:

28070

AN:

33476

American (AMR)

AF:

0.872

AC:

38973

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.755

AC:

19738

AN:

26132

East Asian (EAS)

AF:

0.665

AC:

26400

AN:

39680

South Asian (SAS)

AF:

0.763

AC:

65842

AN:

86238

European-Finnish (FIN)

AF:

0.824

AC:

43733

AN:

53076

Middle Eastern (MID)

AF:

0.695

AC:

4004

AN:

5764

European-Non Finnish (NFE)

AF:

0.780

AC:

866880

AN:

1111812

Other (OTH)

AF:

0.774

AC:

46724

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

17088

34176

51264

68352

85440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20598

41196

61794

82392

102990

<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:

0.801

AC:

121818

AN:

152150

Hom.:

48879

Cov.:

AF XY:

0.801

AC XY:

59562

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.840

AC:

34897

AN:

41530

American (AMR)

AF:

0.827

AC:

12630

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.769

AC:

2668

AN:

3468

East Asian (EAS)

AF:

0.683

AC:

3524

AN:

5156

South Asian (SAS)

AF:

0.773

AC:

3731

AN:

4826

European-Finnish (FIN)

AF:

0.813

AC:

8625

AN:

10604

Middle Eastern (MID)

AF:

0.699

AC:

204

AN:

292

European-Non Finnish (NFE)

AF:

0.783

AC:

53231

AN:

67980

Other (OTH)

AF:

0.792

AC:

1672

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1288

2576

3864

5152

6440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<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:

0.796

Hom.:

16545

Bravo

AF:

0.801

Asia WGS

AF:

0.761

AC:

2648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.8

(source)

DANN

Benign

0.61

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism (auto)

(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

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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