20-13137100-A-T

Position:

• chr20-13137100-A-T

Variant summary

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

The NM_018327.4(SPTLC3):​c.1279+10383A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,068 control chromosomes in the GnomAD database, including 39,626 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 0.72 (39626 hom., cov: 32)
• Consequence: SPTLC3 NM_018327.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPTLC3	NM_018327.4	c.1279+10383A>T		intron_variant		ENST00000399002.7	NP_060797.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPTLC3	ENST00000399002.7	c.1279+10383A>T		intron_variant		1	NM_018327.4	ENSP00000381968.2
SPTLC3	ENST00000431275.1	c.70+10383A>T		intron_variant		2		ENSP00000409760.1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109422 AN: 151950 Hom.: 39577 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.720 AC: 109534 AN: 152068 Hom.: 39626 Cov.: 32 AF XY: 0.721 AC XY: 53625 AN XY: 74328

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.698

Alfa AF: 0.699 Hom.: 4652

Bravo AF: 0.720

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.56

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: rs6105044; hg19: chr20-13117747;