chr3-57928451-T-C

Position:

• chr3-57928451-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.*1162T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,930 control chromosomes in the GnomAD database, including 7,672 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 (7672 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLMAP NM_001377540.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLMAP	NM_001377540.1	c.*1162T>C		3_prime_UTR_variant	25/25	ENST00000671191.1	NP_001364469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLMAP	ENST00000671191.1	c.*1162T>C		3_prime_UTR_variant	25/25		NM_001377540.1	ENSP00000499458	P4

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47180 AN: 151812 Hom.: 7659 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.324

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.311 AC: 47229 AN: 151930 Hom.: 7672 Cov.: 32 AF XY: 0.317 AC XY: 23557 AN XY: 74240

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.323

Alfa AF: 0.260 Hom.: 5097

Bravo AF: 0.317

Asia WGS AF: 0.425 AC: 1482 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.83

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: rs1043045; hg19: chr3-57914178;