rs10930335

chr2-168674036-G-Achr2-168674036-G-C

Variant summary

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

The NM_203463.3(CERS6):c.466-16998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,192 control chromosomes in the GnomAD database, including 63,756 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 0.92 (63756 hom., cov: 31)
• Consequence: CERS6 NM_203463.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

CERS6 (HGNC:23826): (ceramide synthase 6) Enables sphingosine N-acyltransferase activity. Involved in ceramide biosynthetic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CERS6	NM_203463.3	c.466-16998G>A		intron_variant		ENST00000305747.11
CERS6	NM_001256126.2	c.466-16998G>A		intron_variant
CERS6	XM_005246440.6	c.-111-16998G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CERS6	ENST00000305747.11	c.466-16998G>A		intron_variant		2	NM_203463.3	A1
CERS6	ENST00000392687.4	c.466-16998G>A		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139161 AN: 152074 Hom.: 63702 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.915 AC: 139271 AN: 152192 Hom.: 63756 Cov.: 31 AF XY: 0.914 AC XY: 68029 AN XY: 74400

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.893

Alfa AF: 0.908 Hom.: 62460

Bravo AF: 0.920

Asia WGS AF: 0.921 AC: 3205 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	9.5
Dann	Benign	0.78

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: rs10930335; hg19: chr2-169530546;