NM_024552.3:c.1096G>A

Variant names:

• chr19-8262020-G-A
• rs36259
• NM_024552.3:c.1096G>A

Variant summary

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

The NM_024552.3(CERS4):​c.1096G>A​(p.Ala366Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,583,458 control chromosomes in the GnomAD database, including 454,121 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.74 (42222 hom., cov: 35)
  • Exomes 𝑓: 0.76 (411899 hom.)
• Consequence: CERS4 NM_024552.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 43 publications found

Genes affected

CERS4 (HGNC:23747): (ceramide synthase 4) Enables sphingosine N-acyltransferase activity. Involved in ceramide biosynthetic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=1.0931072E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024552.3. 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
	CERS4	NM_024552.3	MANE Select	c.1096G>A	p.Ala366Thr	missense	Exon 12 of 12	NP_078828.2	Q9HA82

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CERS4	ENST00000251363.10	TSL:1 MANE Select	c.1096G>A	p.Ala366Thr	missense	Exon 12 of 12	ENSP00000251363.5	Q9HA82
	CERS4	ENST00000559336.5	TSL:1	c.832G>A	p.Ala278Thr	missense	Exon 10 of 10	ENSP00000453815.1	H0YN04
	CERS4	ENST00000595722.5	TSL:1	n.1425G>A		non_coding_transcript_exon	Exon 13 of 13

Frequencies

GnomAD3 genomes AF: 0.743 AC: 113077 AN: 152124 Hom.: 42191 Cov.: 35

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.765

GnomAD2 exomes AF: 0.750 AC: 166419 AN: 221872 AF XY: 0.753

Gnomad AFR exome AF: 0.682

Gnomad AMR exome AF: 0.700

Gnomad ASJ exome AF: 0.810

Gnomad EAS exome AF: 0.801

Gnomad FIN exome AF: 0.748

Gnomad NFE exome AF: 0.762

Gnomad OTH exome AF: 0.775

GnomAD4 exome AF: 0.758 AC: 1085015 AN: 1431214 Hom.: 411899 Cov.: 75 AF XY: 0.758 AC XY: 538264 AN XY: 710280

African (AFR) AF: 0.670 AC: 21570 AN: 32188

American (AMR) AF: 0.712 AC: 27363 AN: 38430

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 19523 AN: 24122

East Asian (EAS) AF: 0.814 AC: 32141 AN: 39484

South Asian (SAS) AF: 0.736 AC: 60067 AN: 81592

European-Finnish (FIN) AF: 0.745 AC: 38921 AN: 52258

Middle Eastern (MID) AF: 0.783 AC: 4396 AN: 5612

European-Non Finnish (NFE) AF: 0.761 AC: 835948 AN: 1098540

Other (OTH) AF: 0.764 AC: 45086 AN: 58988

GnomAD4 genome AF: 0.743 AC: 113161 AN: 152244 Hom.: 42222 Cov.: 35 AF XY: 0.746 AC XY: 55509 AN XY: 74430

African (AFR) AF: 0.683 AC: 28383 AN: 41540

American (AMR) AF: 0.770 AC: 11776 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4135 AN: 5168

South Asian (SAS) AF: 0.757 AC: 3654 AN: 4828

European-Finnish (FIN) AF: 0.754 AC: 8000 AN: 10616

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51747 AN: 68002

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.759 Hom.: 138012

Bravo AF: 0.741

TwinsUK AF: 0.755 AC: 2800

ALSPAC AF: 0.765 AC: 2947

ESP6500AA AF: 0.690 AC: 3039

ESP6500EA AF: 0.765 AC: 6572

ExAC AF: 0.744 AC: 90078

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.73	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.5
DANN	Benign	0.71
DEOGEN2	Benign	0.089	T
Eigen	Benign	-0.94
Eigen_PC	Benign	-0.97
FATHMM_MKL	Benign	0.048	N
LIST_S2	Benign	0.51	T
MetaRNN	Benign	0.0000011	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	2.0	M
PhyloP100		0.97
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.21	N
REVEL	Benign	0.063
Sift	Benign	0.58	T
Sift4G	Benign	0.59	T
Polyphen		0.012	B
Vest4		0.088
MPC		0.060
ClinPred		0.0041	T
GERP RS		0.91
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.048
gMVP		0.17
Mutation Taster		=98/2	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: rs36259; hg19: chr19-8326904; COSMIC: COSV52167244; COSMIC: COSV52167244;