10-50600853-C-T

Variant names:

• chr10-50600853-C-T
• rs17581623
• NM_147156.4:c.-683-10606G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_147156.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGMS1	NM_147156.4	MANE Select	c.-683-10606G>A		intron	N/A	NP_671512.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGMS1	ENST00000361781.7	TSL:1 MANE Select	c.-683-10606G>A		intron	N/A	ENSP00000354829.2
	SGMS1	ENST00000619438.4	TSL:5	c.-683-10606G>A		intron	N/A	ENSP00000479633.1
	SGMS1	ENST00000429490.5	TSL:5	c.-683-10606G>A		intron	N/A	ENSP00000406795.2

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

African (AFR) AF: 0.0451 AC: 1871 AN: 41528

American (AMR) AF: 0.0955 AC: 1460 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0406 AC: 196 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1315 AN: 10562

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0999 AC: 6790 AN: 67994

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0893 Hom.: 139

Bravo AF: 0.0755

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.39
PhyloP100		-3.5
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: rs17581623; hg19: chr10-52360613;