rs1002666

Variant names:

• chr2-168621508-T-C
• rs1002666
• NM_203463.3:c.408-9477T>C

Variant summary

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

The NM_203463.3(CERS6):​c.408-9477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,064 control chromosomes in the GnomAD database, including 7,866 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 0.30 (7866 hom., cov: 32)
• Consequence: CERS6 NM_203463.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CERS6	NM_203463.3	c.408-9477T>C		intron_variant	Intron 3 of 9	ENST00000305747.11	NP_982288.1
CERS6	NM_001256126.2	c.408-9477T>C		intron_variant	Intron 3 of 10		NP_001243055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CERS6	ENST00000305747.11	c.408-9477T>C		intron_variant	Intron 3 of 9	2	NM_203463.3	ENSP00000306579.6
CERS6	ENST00000392687.4	c.408-9477T>C		intron_variant	Intron 3 of 10	1		ENSP00000376453.4

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46003 AN: 151946 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.303 AC: 46037 AN: 152064 Hom.: 7866 Cov.: 32 AF XY: 0.304 AC XY: 22618 AN XY: 74310

African (AFR) AF: 0.465 AC: 19264 AN: 41442

American (AMR) AF: 0.197 AC: 3014 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3470

East Asian (EAS) AF: 0.168 AC: 866 AN: 5170

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2785 AN: 10554

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16327 AN: 67994

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.259 Hom.: 2459

Bravo AF: 0.298

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.21
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: rs1002666; hg19: chr2-169478018;