12-50130181-T-A

Variant names:

• chr12-50130181-T-A
• rs7532
• NM_147190.5:c.*364A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_147190.5(CERS5):​c.*364A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CERS5 NM_147190.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 18 publications found

Genes affected

CERS5 (HGNC:23749): (ceramide synthase 5) This gene encodes a protein that belongs to the TLC (TRAM, LAG1 and CLN8 homology domains) family of proteins. The encoded protein functions in the synthesis of ceramide, a lipid molecule that is involved in a several cellular signaling pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ENSG00000272368 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_147190.5. 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
	CERS5	NM_147190.5	MANE Select	c.*364A>T		3_prime_UTR	Exon 10 of 10	NP_671723.1	Q8N5B7-1
	CERS5	NM_001331070.3		c.*500A>T		3_prime_UTR	Exon 11 of 11	NP_001317999.1
	CERS5	NM_001331071.3		c.*500A>T		3_prime_UTR	Exon 11 of 11	NP_001318000.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CERS5	ENST00000317551.12	TSL:2 MANE Select	c.*364A>T		3_prime_UTR	Exon 10 of 10	ENSP00000325485.6	Q8N5B7-1
	CERS5	ENST00000380189.8	TSL:1	n.*2004A>T		non_coding_transcript_exon	Exon 10 of 10	ENSP00000369536.4	Q49AQ3
	CERS5	ENST00000380189.8	TSL:1	n.*2004A>T		3_prime_UTR	Exon 10 of 10	ENSP00000369536.4	Q49AQ3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 24110 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12472

African (AFR) AF: 0.00 AC: 0 AN: 830

American (AMR) AF: 0.00 AC: 0 AN: 1226

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 894

East Asian (EAS) AF: 0.00 AC: 0 AN: 1268

South Asian (SAS) AF: 0.00 AC: 0 AN: 716

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 112

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 15898

Other (OTH) AF: 0.00 AC: 0 AN: 1594

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.53
PhyloP100		0.68

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: rs7532; hg19: chr12-50523964;