rs36212407

Positions:

• chr10-122846150-C-T

Variant summary

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

The ENST00000368904.6(ENSG00000286088):​n.-307G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 285,780 control chromosomes in the GnomAD database, including 1,727 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 0.088 (806 hom., cov: 33)
  • Exomes 𝑓: 0.11 (921 hom.)
• Consequence: ENSG00000286088 ENST00000368904.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

Genes affected

CUZD1 (HGNC:17937): (CUB and zona pellucida like domains 1) Predicted to be involved in trypsinogen activation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM24B-CUZD1	NR_037915.1	n.370G>A		non_coding_transcript_exon_variant	3/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286088	ENST00000368904.6	n.-307G>A		non_coding_transcript_exon_variant	2/10	1		ENSP00000357900.2
ENSG00000286088	ENST00000368904.6	n.-307G>A		5_prime_UTR_variant	2/10	1		ENSP00000357900.2

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13460 AN: 152192 Hom.: 808 Cov.: 33

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.112 AC: 14951 AN: 133470 Hom.: 921 Cov.: 0 AF XY: 0.111 AC XY: 7576 AN XY: 68142

Gnomad4 AFR exome AF: 0.0315

Gnomad4 AMR exome AF: 0.126

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.000114

Gnomad4 SAS exome AF: 0.0750

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.126

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0883 AC: 13454 AN: 152310 Hom.: 806 Cov.: 33 AF XY: 0.0880 AC XY: 6556 AN XY: 74478

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0614

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.106

Alfa AF: 0.104 Hom.: 293

Bravo AF: 0.0838

Asia WGS AF: 0.0290 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs36212407; hg19: chr10-124605666;