rs6760875

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142644.2(SPHKAP):​c.247-33639T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,138 control chromosomes in the GnomAD database, including 34,524 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 0.67 ( 34524 hom., cov: 33)

Consequence

SPHKAP
NM_001142644.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.895
Variant links:
Genes affected
SPHKAP (HGNC:30619): (SPHK1 interactor, AKAP domain containing) Enables protein kinase A binding activity. Predicted to be located in Z disc. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SPHKAPNM_001142644.2 linkuse as main transcriptc.247-33639T>C intron_variant ENST00000392056.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SPHKAPENST00000392056.8 linkuse as main transcriptc.247-33639T>C intron_variant 1 NM_001142644.2 P2Q2M3C7-1
SPHKAPENST00000344657.5 linkuse as main transcriptc.247-33639T>C intron_variant 1 A2Q2M3C7-2

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
101883
AN:
152020
Hom.:
34465
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.775
Gnomad AMI
AF:
0.819
Gnomad AMR
AF:
0.692
Gnomad ASJ
AF:
0.697
Gnomad EAS
AF:
0.647
Gnomad SAS
AF:
0.730
Gnomad FIN
AF:
0.647
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.599
Gnomad OTH
AF:
0.669
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.671
AC:
102010
AN:
152138
Hom.:
34524
Cov.:
33
AF XY:
0.673
AC XY:
50095
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.775
Gnomad4 AMR
AF:
0.693
Gnomad4 ASJ
AF:
0.697
Gnomad4 EAS
AF:
0.647
Gnomad4 SAS
AF:
0.731
Gnomad4 FIN
AF:
0.647
Gnomad4 NFE
AF:
0.599
Gnomad4 OTH
AF:
0.673
Alfa
AF:
0.613
Hom.:
58008
Bravo
AF:
0.675
Asia WGS
AF:
0.729
AC:
2536
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.72
DANN
Benign
0.28

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: rs6760875; hg19: chr2-228925898; API