rs267735

Variant names:

• chr1-150976020-T-A
• rs267735
• ENST00000911844.1:c.-2+1018A>T

Variant summary

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

The ENST00000911844.1(CERS2):​c.-2+1018A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 149,772 control chromosomes in the GnomAD database, including 14,452 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 0.41 (14452 hom., cov: 31)
• Consequence: CERS2 ENST00000911844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 8 publications found

Genes affected

CERS2 (HGNC:14076): (ceramide synthase 2) This gene encodes a protein that has sequence similarity to yeast longevity assurance gene 1. Mutation or overexpression of the related gene in yeast has been shown to alter yeast lifespan. The human protein may play a role in the regulation of cell growth. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

ENSG00000231073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000911844.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CERS2	ENST00000911844.1		c.-2+1018A>T		intron	N/A	ENSP00000581903.1
	CERS2	ENST00000911845.1		c.-2+206A>T		intron	N/A	ENSP00000581904.1
	ENSG00000231073	ENST00000808151.1		n.309-1281T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 61719 AN: 149676 Hom.: 14456 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.412 AC: 61720 AN: 149772 Hom.: 14452 Cov.: 31 AF XY: 0.410 AC XY: 29969 AN XY: 73110

African (AFR) AF: 0.178 AC: 7231 AN: 40656

American (AMR) AF: 0.373 AC: 5614 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1431 AN: 3442

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5160

South Asian (SAS) AF: 0.350 AC: 1658 AN: 4738

European-Finnish (FIN) AF: 0.561 AC: 5703 AN: 10166

Middle Eastern (MID) AF: 0.433 AC: 123 AN: 284

European-Non Finnish (NFE) AF: 0.541 AC: 36399 AN: 67306

Other (OTH) AF: 0.437 AC: 905 AN: 2072

Alfa AF: 0.468 Hom.: 2267

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.12
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs267735; hg19: chr1-150948496;