dbSNP rs8020841: SLC8A3:c.*505A>G (chr14-70045442-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_182932.3(SLC8A3):c.*505A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,198 control chromosomes in the GnomAD database, including 5,189 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 0.26 ( 5184 hom., cov: 32)

Exomes 𝑓: 0.19 ( 5 hom. )

Consequence

SLC8A3
NM_182932.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.462

Publications

4 publications found

Variant links:

Genes affected

SLC8A3 (HGNC:11070): (solute carrier family 8 member A3) This gene encodes a member of the sodium/calcium exchanger integral membrane protein family. Na+/Ca2+ exchange proteins are involved in maintaining Ca2+ homeostasis in a wide variety of cell types. The protein is regulated by intracellular calcium ions and is found in both the plasma membrane and intracellular organellar membranes, where exchange of Na+ for Ca2+ occurs in an electrogenic manner. Alternative splicing has been observed for this gene and multiple variants have been described. [provided by RefSeq, Aug 2013]

SLC8A3 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182932.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC8A3	NM_182932.3	MANE Select	c.*505A>G	3_prime_UTR	Exon 7 of 7	NP_891977.1	P57103-2
SLC8A3	NM_183002.3		c.*505A>G	3_prime_UTR	Exon 8 of 8	NP_892114.1	P57103-1
SLC8A3	NM_033262.5		c.*505A>G	3_prime_UTR	Exon 8 of 8	NP_150287.1	P57103-7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC8A3	ENST00000356921.7	TSL:1 MANE Select	c.*505A>G	3_prime_UTR	Exon 7 of 7	ENSP00000349392.3	P57103-2
SLC8A3	ENST00000381269.6	TSL:1	c.*505A>G	3_prime_UTR	Exon 8 of 8	ENSP00000370669.2	P57103-1
SLC8A3	ENST00000216568.11	TSL:1	c.*505A>G	3_prime_UTR	Exon 6 of 6	ENSP00000216568.7	P57103-5

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38751

AN:

151848

Hom.:

5173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.0574

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.185

AC:

AN:

232

Hom.:

Cov.:

AF XY:

0.113

AC XY:

AN XY:

106

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.182

AC:

AN:

170

Other (OTH)

AF:

0.182

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

AF:

0.255

AC:

38799

AN:

151966

Hom.:

5184

Cov.:

AF XY:

0.252

AC XY:

18738

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.326

AC:

13486

AN:

41418

American (AMR)

AF:

0.204

AC:

3112

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

798

AN:

3466

East Asian (EAS)

AF:

0.0572

AC:

296

AN:

5178

South Asian (SAS)

AF:

0.114

AC:

549

AN:

4804

European-Finnish (FIN)

AF:

0.289

AC:

3052

AN:

10550

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.246

AC:

16725

AN:

67966

Other (OTH)

AF:

0.249

AC:

525

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1494

2989

4483

5978

7472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

390

780

1170

1560

1950

<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:

0.244

Hom.:

12190

Bravo

AF:

0.253

Asia WGS

AF:

0.129

AC:

448

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.43

(source)

DANN

Benign

0.56

PhyloP100

-0.46

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

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