10-50600853-C-T

Position:

• chr10-50600853-C-T

Variant summary

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

The NM_147156.4(SGMS1):​c.-683-10606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 152,168 control chromosomes in the GnomAD database, including 603 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 0.081 (603 hom., cov: 32)
• Consequence: SGMS1 NM_147156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

Genes affected

SGMS1 (HGNC:29799): (sphingomyelin synthase 1) The protein encoded by this gene is predicted to be a five-pass transmembrane protein. This gene may be predominately expressed in brain. [provided by RefSeq, Jul 2008]

SGMS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGMS1	NM_147156.4	c.-683-10606G>A		intron_variant		ENST00000361781.7	NP_671512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGMS1	ENST00000361781.7	c.-683-10606G>A		intron_variant		1	NM_147156.4	ENSP00000354829.2

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12367 AN: 152050 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0812 AC: 12362 AN: 152168 Hom.: 603 Cov.: 32 AF XY: 0.0809 AC XY: 6021 AN XY: 74386

Gnomad4 AFR AF: 0.0451

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0999

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0903 Hom.: 139

Bravo AF: 0.0755

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.39

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: rs17581623; hg19: chr10-52360613;