GeneBe

rs10611760

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_021097.5(SLC8A1):​c.2269+4261_2269+4264del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.96 ( 69756 hom., cov: 0)

Consequence

SLC8A1
NM_021097.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.75
Variant links:
Genes affected
SLC8A1 (HGNC:11068): (solute carrier family 8 member A1) In cardiac myocytes, Ca(2+) concentrations alternate between high levels during contraction and low levels during relaxation. The increase in Ca(2+) concentration during contraction is primarily due to release of Ca(2+) from intracellular stores. However, some Ca(2+) also enters the cell through the sarcolemma (plasma membrane). During relaxation, Ca(2+) is sequestered within the intracellular stores. To prevent overloading of intracellular stores, the Ca(2+) that entered across the sarcolemma must be extruded from the cell. The Na(+)-Ca(2+) exchanger is the primary mechanism by which the Ca(2+) is extruded from the cell during relaxation. In the heart, the exchanger may play a key role in digitalis action. The exchanger is the dominant mechanism in returning the cardiac myocyte to its resting state following excitation.[supplied by OMIM, Apr 2004]
SLC8A1-AS1 (HGNC:44102): (SLC8A1 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC8A1NM_021097.5 linkuse as main transcriptc.2269+4261_2269+4264del intron_variant ENST00000332839.9
SLC8A1-AS1NR_038441.1 linkuse as main transcriptn.121+51544_121+51547del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC8A1ENST00000332839.9 linkuse as main transcriptc.2269+4261_2269+4264del intron_variant 1 NM_021097.5 P4P32418-1
SLC8A1-AS1ENST00000599740.1 linkuse as main transcriptn.74-95178_74-95175del intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.957
AC:
145142
AN:
151650
Hom.:
69708
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.875
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.985
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
0.822
Gnomad SAS
AF:
0.980
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.987
Gnomad NFE
AF:
0.999
Gnomad OTH
AF:
0.962
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.957
AC:
145247
AN:
151770
Hom.:
69756
Cov.:
0
AF XY:
0.957
AC XY:
71008
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.875
Gnomad4 AMR
AF:
0.985
Gnomad4 ASJ
AF:
1.00
Gnomad4 EAS
AF:
0.822
Gnomad4 SAS
AF:
0.980
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.999
Gnomad4 OTH
AF:
0.957
Alfa
AF:
0.975
Hom.:
7770
Bravo
AF:
0.950
Asia WGS
AF:
0.903
AC:
3138
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10611760; hg19: chr2-40383640; API