20-13143086-T-G

Position:

• chr20-13143086-T-G

Variant summary

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

The NM_018327.4(SPTLC3):​c.1280-10917T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,254 control chromosomes in the GnomAD database, including 1,110 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 0.11 (1110 hom., cov: 32)
• Consequence: SPTLC3 NM_018327.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPTLC3	NM_018327.4	c.1280-10917T>G		intron_variant		ENST00000399002.7	NP_060797.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPTLC3	ENST00000399002.7	c.1280-10917T>G		intron_variant		1	NM_018327.4	ENSP00000381968.2
SPTLC3	ENST00000431275.1	c.71-10917T>G		intron_variant		2		ENSP00000409760.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17407 AN: 152136 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.114 AC: 17422 AN: 152254 Hom.: 1110 Cov.: 32 AF XY: 0.117 AC XY: 8701 AN XY: 74442

Gnomad4 AFR AF: 0.0628

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.102

Alfa AF: 0.128 Hom.: 1717

Bravo AF: 0.118

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.79

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: rs17190927; hg19: chr20-13123733;