1-32205429-C-T

Position:

• chr1-32205429-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000373604.4(ENSG00000224066):​n.72-90G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0928 in 790,224 control chromosomes in the GnomAD database, including 4,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (1030 hom., cov: 32)
  • Exomes 𝑓: 0.090 (3694 hom.)
• Consequence: ENST00000373604.4 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.967

Genes affected

(HGNC:):

CCDC28B (HGNC:28163): (coiled-coil domain containing 28B) The product of this gene localizes to centrosomes and basal bodies. The protein colocalizes with several proteins associated with Bardet-Biedl syndrome (BBS) and participates in the regulation of cilia development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 1-32205429-C-T is Benign according to our data. Variant chr1-32205429-C-T is described in ClinVar as [Benign]. Clinvar id is 1253098.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC28B	NM_024296.5			downstream_gene_variant		ENST00000373602.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000373604.4	n.72-90G>A		intron_variant, non_coding_transcript_variant		3
CCDC28B	ENST00000373602.10			downstream_gene_variant		1	NM_024296.5	P1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15769 AN: 152110 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0975

GnomAD4 exome AF: 0.0901 AC: 57512 AN: 637996 Hom.: 3694 Cov.: 9 AF XY: 0.0953 AC XY: 30967 AN XY: 325026

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.0686

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.228

Gnomad4 FIN exome AF: 0.0985

Gnomad4 NFE exome AF: 0.0629

Gnomad4 OTH exome AF: 0.0919

GnomAD4 genome AF: 0.104 AC: 15791 AN: 152228 Hom.: 1030 Cov.: 32 AF XY: 0.109 AC XY: 8111 AN XY: 74422

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0688

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0697 Hom.: 465

Bravo AF: 0.103

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.0
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295116; hg19: chr1-32671030;