Variant 2-168715009-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_203463.3(CERS6):c.618C>T(p.Gly206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00959 in 1,603,254 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 4 hom., cov: 32)

Exomes 𝑓: 0.010 ( 115 hom. )

Consequence

CERS6
NM_203463.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0500

Variant links:

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]

CERS6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 2-168715009-C-T is Benign according to our data. Variant chr2-168715009-C-T is described in ClinVar as [Benign]. Clinvar id is 769263.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.05 with no splicing effect.

BS2

High AC in GnomAd4 at 899 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CERS6	NM_203463.3 linkuse as main transcript	c.618C>T	p.Gly206=	synonymous_variant	7/10	ENST00000305747.11
CERS6	NM_001256126.2 linkuse as main transcript	c.618C>T	p.Gly206=	synonymous_variant	7/11
CERS6	XM_017003749.3 linkuse as main transcript	c.195C>T	p.Gly65=	synonymous_variant	4/8
CERS6	XM_005246440.6 linkuse as main transcript	c.42C>T	p.Gly14=	synonymous_variant	4/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CERS6	ENST00000305747.11 linkuse as main transcript	c.618C>T	p.Gly206=	synonymous_variant	7/10	2	NM_203463.3	A1	Q6ZMG9-1
CERS6	ENST00000392687.4 linkuse as main transcript	c.618C>T	p.Gly206=	synonymous_variant	7/11	1		P4	Q6ZMG9-2

Frequencies

GnomAD3 genomes

AF:

0.00591

AC:

899

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00207

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00459

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00562

AC:

1354

AN:

241044

Hom.:

AF XY:

0.00567

AC XY:

738

AN XY:

130242

show subpopulations

Gnomad AFR exome

AF:

0.00195

Gnomad AMR exome

AF:

0.00358

Gnomad ASJ exome

AF:

0.00113

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000217

Gnomad FIN exome

AF:

0.000841

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.00667

GnomAD4 exome

AF:

0.00997

AC:

14471

AN:

1450958

Hom.:

115

Cov.:

AF XY:

0.00954

AC XY:

6879

AN XY:

721426

show subpopulations

Gnomad4 AFR exome

AF:

0.00143

Gnomad4 AMR exome

AF:

0.00361

Gnomad4 ASJ exome

AF:

0.00136

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000312

Gnomad4 FIN exome

AF:

0.000789

Gnomad4 NFE exome

AF:

0.0124

Gnomad4 OTH exome

AF:

0.00677

GnomAD4 genome

AF:

0.00590

AC:

899

AN:

152296

Hom.:

Cov.:

AF XY:

0.00522

AC XY:

389

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00207

Gnomad4 AMR

AF:

0.00458

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00814

Hom.:

Bravo

AF:

0.00611

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

3.9

DANN

Benign

0.54

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over