9-92107870-C-A

Variant names:

• chr9-92107870-C-A
• rs1970121
• NM_006415.4:c.260+870G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006415.4(SPTLC1):​c.260+870G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,084 control chromosomes in the GnomAD database, including 9,627 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 (9627 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPTLC1 NM_006415.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

Genes affected

SPTLC1 (HGNC:11277): (serine palmitoyltransferase long chain base subunit 1) This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]

SPTLC1 Gene-Disease associations (from GenCC):

• amyotrophic lateral sclerosis 27, juvenile

  Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• neuropathy, hereditary sensory and autonomic, type 1A

  Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
• hereditary sensory and autonomic neuropathy type 1

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006415.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPTLC1	NM_006415.4	MANE Select	c.260+870G>T		intron	N/A	NP_006406.1	O15269-1
	SPTLC1	NM_001281303.2		c.260+870G>T		intron	N/A	NP_001268232.1
	SPTLC1	NM_001368272.1		c.-240+870G>T		intron	N/A	NP_001355201.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPTLC1	ENST00000262554.7	TSL:1 MANE Select	c.260+870G>T		intron	N/A	ENSP00000262554.2	O15269-1
	SPTLC1	ENST00000337841.4	TSL:1	c.260+870G>T		intron	N/A	ENSP00000337635.4	O15269-2
	SPTLC1	ENST00000461132.2	TSL:2	c.*866G>T		3_prime_UTR	Exon 3 of 3	ENSP00000509096.1	A0A8I5KWE0

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46449 AN: 151966 Hom.: 9596 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.284

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.306 AC: 46533 AN: 152084 Hom.: 9627 Cov.: 33 AF XY: 0.307 AC XY: 22799 AN XY: 74370

African (AFR) AF: 0.579 AC: 24023 AN: 41456

American (AMR) AF: 0.323 AC: 4934 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1899 AN: 5178

South Asian (SAS) AF: 0.262 AC: 1266 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2033 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10622 AN: 67980

Other (OTH) AF: 0.289 AC: 610 AN: 2110

Alfa AF: 0.242 Hom.: 930

Bravo AF: 0.327

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.15
PhyloP100		-1.9
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: rs1970121; hg19: chr9-94870152;