3-57794109-T-C

Position:

• chr3-57794109-T-C

Variant summary

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

The NM_001377540.1(SLMAP):​c.198+36260T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,002 control chromosomes in the GnomAD database, including 11,076 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 0.36 (11076 hom., cov: 31)
• Consequence: SLMAP NM_001377540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

SLMAP (HGNC:16643): (sarcolemma associated protein) This gene encodes a component of a conserved striatin-interacting phosphatase and kinase complex. Striatin family complexes participate in a variety of cellular processes including signaling, cell cycle control, cell migration, Golgi assembly, and apoptosis. The protein encoded by this gene is a coiled-coil, tail-anchored membrane protein with a single C-terminal transmembrane domain that is posttranslationally inserted into membranes. Mutations in this gene are associated with Brugada syndrome, a cardiac channelopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLMAP	NM_001377540.1	c.198+36260T>C		intron_variant		ENST00000671191.1	NP_001364469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLMAP	ENST00000671191.1	c.198+36260T>C		intron_variant			NM_001377540.1	ENSP00000499458	P4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55331 AN: 151882 Hom.: 11086 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.393

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55329 AN: 152002 Hom.: 11076 Cov.: 31 AF XY: 0.371 AC XY: 27558 AN XY: 74266

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.391

Alfa AF: 0.402 Hom.: 10929

Bravo AF: 0.352

Asia WGS AF: 0.558 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.80

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: rs6768930; hg19: chr3-57779836;