rs3811514

chr2-228019005-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142644.2(SPHKAP):c.1849A>G(p.Lys617Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,613,484 control chromosomes in the GnomAD database, including 225,334 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.59 (26964 hom., cov: 32)
  • Exomes 𝑓: 0.52 (198370 hom.)
• Consequence: SPHKAP NM_001142644.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

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]

LOC105373918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.3734482E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPHKAP	NM_001142644.2	c.1849A>G	p.Lys617Glu	missense_variant	7/12	ENST00000392056.8
LOC105373918	XR_001739908.2	n.147-7976T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPHKAP	ENST00000392056.8	c.1849A>G	p.Lys617Glu	missense_variant	7/12	1	NM_001142644.2	P2
SPHKAP	ENST00000344657.5	c.1849A>G	p.Lys617Glu	missense_variant	7/11	1		A2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88989 AN: 151966 Hom.: 26911 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.574

GnomAD3 exomes AF: 0.575 AC: 143356 AN: 249500 Hom.: 42513 AF XY: 0.566 AC XY: 76393 AN XY: 134952

Gnomad AFR exome AF: 0.748

Gnomad AMR exome AF: 0.733

Gnomad ASJ exome AF: 0.553

Gnomad EAS exome AF: 0.626

Gnomad SAS exome AF: 0.619

Gnomad FIN exome AF: 0.515

Gnomad NFE exome AF: 0.496

Gnomad OTH exome AF: 0.543

GnomAD4 exome AF: 0.516 AC: 754541 AN: 1461400 Hom.: 198370 Cov.: 80 AF XY: 0.518 AC XY: 376850 AN XY: 726966

Gnomad4 AFR exome AF: 0.743

Gnomad4 AMR exome AF: 0.721

Gnomad4 ASJ exome AF: 0.547

Gnomad4 EAS exome AF: 0.622

Gnomad4 SAS exome AF: 0.616

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.488

Gnomad4 OTH exome AF: 0.533

GnomAD4 genome AF: 0.586 AC: 89104 AN: 152084 Hom.: 26964 Cov.: 32 AF XY: 0.587 AC XY: 43659 AN XY: 74328

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.573

Alfa AF: 0.524 Hom.: 37165

Bravo AF: 0.602

TwinsUK AF: 0.494 AC: 1830

ALSPAC AF: 0.482 AC: 1857

ESP6500AA AF: 0.737 AC: 3248

ESP6500EA AF: 0.499 AC: 4291

ExAC AF: 0.572 AC: 69395

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.056
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.5
Dann	Benign	0.16
DEOGEN2	Benign	0.016	T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-0.96
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.042	T;T
MetaRNN	Benign	0.0000014	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-2.4	N;N
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.29	T
PROVEAN	Benign	1.5	N;N
REVEL	Benign	0.13
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.027
MPC		0.061
ClinPred		0.0019	T
GERP RS		4.0
Varity_R		0.070
gMVP		0.31

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

Other links and lift over

dbSNP: rs3811514; hg19: chr2-228883721; COSMIC: COSV60870928;