rs60774903

chr19-18896790-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387442.1(CERS1):c.-275C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,398 control chromosomes in the GnomAD database, including 4,839 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 0.21 (4838 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: CERS1 NM_001387442.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

Genes affected

CERS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CERS1	NM_001290265.2	c.-275C>A		5_prime_UTR_variant	1/6
CERS1	NM_001387442.1	c.-275C>A		5_prime_UTR_variant	1/7
CERS1	NM_001387443.1	c.-110C>A		5_prime_UTR_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31690 AN: 152064 Hom.: 4837 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.116 AC: 25 AN: 216 Hom.: 1 AF XY: 0.117 AC XY: 18 AN XY: 154

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.208 AC: 31704 AN: 152182 Hom.: 4838 Cov.: 32 AF XY: 0.201 AC XY: 14965 AN XY: 74400

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0621

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.176

Alfa AF: 0.178 Hom.: 440

Bravo AF: 0.223

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60774903; hg19: chr19-19007599;