Variant chr2-168714904-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_203463.3(CERS6):c.610-97G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 1,137,022 control chromosomes in the GnomAD database, including 131,462 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 0.37 ( 12608 hom., cov: 32)

Exomes 𝑓: 0.48 ( 118854 hom. )

Consequence

CERS6
NM_203463.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.374

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CERS6	NM_203463.3 linkuse as main transcript	c.610-97G>T	intron_variant	ENST00000305747.11
CERS6	NM_001256126.2 linkuse as main transcript	c.610-97G>T	intron_variant
CERS6	XM_005246440.6 linkuse as main transcript	c.34-97G>T	intron_variant
CERS6	XM_017003749.3 linkuse as main transcript	c.187-97G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CERS6	ENST00000305747.11 linkuse as main transcript	c.610-97G>T		intron_variant		2	NM_203463.3	A1	Q6ZMG9-1
CERS6	ENST00000392687.4 linkuse as main transcript	c.610-97G>T		intron_variant		1		P4	Q6ZMG9-2

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55913

AN:

151878

Hom.:

12611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.366

GnomAD4 exome

AF:

0.480

AC:

473137

AN:

985026

Hom.:

118854

AF XY:

0.482

AC XY:

240638

AN XY:

499302

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.287

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.179

Gnomad4 SAS exome

AF:

0.505

Gnomad4 FIN exome

AF:

0.563

Gnomad4 NFE exome

AF:

0.510

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.368

AC:

55903

AN:

151996

Hom.:

12608

Cov.:

AF XY:

0.372

AC XY:

27648

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.501

Gnomad4 OTH

AF:

0.361

Alfa

AF:

0.376

Hom.:

2509

Bravo

AF:

0.332

Asia WGS

AF:

0.333

AC:

1158

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.041

DANN

Benign

0.52

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over