Genetic Variant SLC24A2:c.*3740G>A (chr9-19512413-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_020344.4(SLC24A2):c.*3740G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,074 control chromosomes in the GnomAD database, including 8,880 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 0.32 ( 8879 hom., cov: 32)

Exomes 𝑓: 0.29 ( 1 hom. )

Consequence

SLC24A2
NM_020344.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.73

Publications

3 publications found

Variant links:

Genes affected

SLC24A2 (HGNC:10976): (solute carrier family 24 member 2) This gene encodes a member of the calcium/cation antiporter superfamily of transport proteins. The encoded protein belongs to the SLC24 branch of exchangers, which can mediate the extrusion of one Ca2+ ion and one K+ ion in exchange for four Na+ ions. This family member is a retinal cone/brain exchanger that can mediate a light-induced decrease in free Ca2+ concentration. This protein may also play a neuroprotective role during ischemic brain injury. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

SLC24A2 links:

LOC105375988 (HGNC:):

LOC105375988 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC24A2	NM_020344.4 link	c.*3740G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000341998.7	NP_065077.1	Q9UI40-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC24A2	ENST00000341998.7 link	c.*3740G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_020344.4	ENSP00000344801.1		Q9UI40-1
SLC24A2	ENST00000286344.4 link	c.*3740G>A		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000286344.3		Q9UI40-2

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48666

AN:

151932

Hom.:

8846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.0419

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.208

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.292

AC:

AN:

Hom.:

Cov.:

AF XY:

0.375

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.321

AC:

48755

AN:

152050

Hom.:

8879

Cov.:

AF XY:

0.329

AC XY:

24413

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.431

AC:

17861

AN:

41482

American (AMR)

AF:

0.400

AC:

6114

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

874

AN:

3470

East Asian (EAS)

AF:

0.580

AC:

2999

AN:

5172

South Asian (SAS)

AF:

0.399

AC:

1917

AN:

4808

European-Finnish (FIN)

AF:

0.343

AC:

3618

AN:

10544

Middle Eastern (MID)

AF:

0.200

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.216

AC:

14684

AN:

67982

Other (OTH)

AF:

0.280

AC:

592

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1647

3293

4940

6586

8233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.275

Hom.:

3698

Bravo

AF:

0.333

Asia WGS

AF:

0.517

AC:

1796

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.72

PhyloP100

-1.7

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over