10-50500034-A-C

Variant names:

• chr10-50500034-A-C
• rs12251514
• NM_147156.4:c.-498+19797T>G

Variant summary

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

The NM_147156.4(SGMS1):​c.-498+19797T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,210 control chromosomes in the GnomAD database, including 201 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 0.038 (201 hom., cov: 33)
• Consequence: SGMS1 NM_147156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0894 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.-498+19797T>G		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.-498+19797T>G		intron	N/A	ENSP00000354829.2
	SGMS1	ENST00000619438.4	TSL:5	c.-498+19797T>G		intron	N/A	ENSP00000479633.1
	SGMS1	ENST00000429490.5	TSL:5	c.-498+19797T>G		intron	N/A	ENSP00000406795.2

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5849 AN: 152092 Hom.: 201 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0187

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0385 AC: 5860 AN: 152210 Hom.: 201 Cov.: 33 AF XY: 0.0386 AC XY: 2872 AN XY: 74442

African (AFR) AF: 0.0918 AC: 3810 AN: 41510

American (AMR) AF: 0.0186 AC: 285 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.0705 AC: 364 AN: 5164

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4828

European-Finnish (FIN) AF: 0.0258 AC: 274 AN: 10614

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 818 AN: 68004

Other (OTH) AF: 0.0317 AC: 67 AN: 2116

Alfa AF: 0.0115 Hom.: 6

Bravo AF: 0.0406

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.57
PhyloP100		-0.86
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: rs12251514; hg19: chr10-52259794;