rs2144134

chr20-13167505-C-G

Variant summary

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

The NM_018327.4(SPTLC3):c.*2638C>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 0.468 in 151,938 control chromosomes in the GnomAD database, including 16,816 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 0.47 (16816 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPTLC3 NM_018327.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

SPTLC3 (HGNC:16253): (serine palmitoyltransferase long chain base subunit 3) This gene encodes a subunit of the serine palmitoyltransferase complex which catalyzes the rate-limiting step in sphingolipid biosynthesis. This subunit metabolizes lauroyl- and myristoyl-CoA and generates C14 and C16-sphingoid bases. [provided by RefSeq, Mar 2017]

TASP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPTLC3	NM_018327.4	c.*2638C>G		3_prime_UTR_variant	12/12	ENST00000399002.7
SPTLC3	NM_001349945.2	c.*2638C>G		3_prime_UTR_variant	13/13
SPTLC3	XM_011529280.2	c.*2638C>G		3_prime_UTR_variant	9/9
TASP1	XR_001754319.3	n.1370-62248G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPTLC3	ENST00000399002.7	c.*2638C>G		3_prime_UTR_variant	12/12	1	NM_018327.4	P1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71066 AN: 151820 Hom.: 16788 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.459

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.468 AC: 71149 AN: 151938 Hom.: 16816 Cov.: 32 AF XY: 0.474 AC XY: 35191 AN XY: 74274

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.460

Alfa AF: 0.460 Hom.: 1998

Bravo AF: 0.471

Asia WGS AF: 0.649 AC: 2256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.78
Dann	Benign	0.60

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: rs2144134; hg19: chr20-13148152;