rs1057719

Variant names:

• chr3-57927987-A-G
• rs1057719
• NM_001377540.1:c.*698A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

SLMAP Gene-Disease associations (from GenCC):

• Brugada syndrome

  Inheritance: Unknown, AD Classification: SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: Genomics England PanelApp, Orphanet, ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377540.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLMAP	NM_001377540.1	MANE Select	c.*698A>G		3_prime_UTR	Exon 25 of 25	NP_001364469.1
	SLMAP	NR_165328.1		n.4271A>G		non_coding_transcript_exon	Exon 23 of 23
	SLMAP	NM_001377538.1		c.*599A>G		3_prime_UTR	Exon 24 of 24	NP_001364467.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLMAP	ENST00000671191.1	MANE Select	c.*698A>G		3_prime_UTR	Exon 25 of 25	ENSP00000499458.1
	SLMAP	ENST00000417128.7	TSL:1	c.*698A>G		3_prime_UTR	Exon 23 of 23	ENSP00000412829.3
	SLMAP	ENST00000449503.6	TSL:1	c.*599A>G		3_prime_UTR	Exon 20 of 20	ENSP00000412945.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.317 AC: 132 AN: 416

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.361 AC: 14879 AN: 41238

American (AMR) AF: 0.350 AC: 5310 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1216 AN: 3458

East Asian (EAS) AF: 0.479 AC: 2471 AN: 5154

South Asian (SAS) AF: 0.373 AC: 1788 AN: 4794

European-Finnish (FIN) AF: 0.302 AC: 3159 AN: 10446

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16792 AN: 67858

Other (OTH) AF: 0.318 AC: 673 AN: 2114

Alfa AF: 0.276 Hom.: 7631

Bravo AF: 0.314

Asia WGS AF: 0.421 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.8
DANN	Benign	0.65
PhyloP100		-0.033
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1057719; hg19: chr3-57913714;