rs1057719

Positions:

• chr3-57927987-A-G

Variant summary

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

The NM_001377540.1(SLMAP):​c.*698A>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 0.308 in 151,872 control chromosomes in the GnomAD database, including 7,509 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 0.31 (7493 hom., cov: 31)
  • Exomes 𝑓: 0.32 (16 hom.)
• Consequence: SLMAP NM_001377540.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLMAP	NM_001377540.1	c.*698A>G		3_prime_UTR_variant	25/25	ENST00000671191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLMAP	ENST00000671191.1	c.*698A>G		3_prime_UTR_variant	25/25		NM_001377540.1	P4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46624 AN: 151332 Hom.: 7483 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.320 AC: 135 AN: 422 Hom.: 16 Cov.: 0 AF XY: 0.327 AC XY: 83 AN XY: 254

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.308 AC: 46663 AN: 151450 Hom.: 7493 Cov.: 31 AF XY: 0.315 AC XY: 23282 AN XY: 73962

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.318

Alfa AF: 0.271 Hom.: 5501

Bravo AF: 0.314

Asia WGS AF: 0.421 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.8
DANN	Benign	0.65

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: rs1057719; hg19: chr3-57913714;