15-78105161-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006383.4(CIB2):c.*149_*150insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 862,032 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0070 (9 hom., cov: 32)
  • Exomes 𝑓: 0.038 (1 hom.)
• Consequence: CIB2 NM_006383.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.945

Genes affected

CIB2 (HGNC:24579): (calcium and integrin binding family member 2) The protein encoded by this gene is similar to that of KIP/CIB, calcineurin B, and calmodulin. The encoded protein is a calcium-binding regulatory protein that interacts with DNA-dependent protein kinase catalytic subunits (DNA-PKcs), and it is involved in photoreceptor cell maintenance. Mutations in this gene cause deafness, autosomal recessive, 48 (DFNB48), and also Usher syndrome 1J (USH1J). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-78105161-G-GT is Benign according to our data. Variant chr15-78105161-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 1198459.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIB2	NM_006383.4	c.*149_*150insA		3_prime_UTR_variant	6/6	ENST00000258930.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIB2	ENST00000258930.8	c.*149_*150insA		3_prime_UTR_variant	6/6	1	NM_006383.4	P1

Frequencies

GnomAD3 genomes AF: 0.00697 AC: 1034 AN: 148444 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00236

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00785

Gnomad SAS AF: 0.00171

Gnomad FIN AF: 0.000303

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000210

Gnomad OTH AF: 0.00542

GnomAD4 exome AF: 0.0376 AC: 26843 AN: 713494 Hom.: 1 Cov.: 12 AF XY: 0.0373 AC XY: 13359 AN XY: 358240

Gnomad4 AFR exome AF: 0.0629

Gnomad4 AMR exome AF: 0.0349

Gnomad4 ASJ exome AF: 0.0413

Gnomad4 EAS exome AF: 0.0403

Gnomad4 SAS exome AF: 0.0365

Gnomad4 FIN exome AF: 0.0358

Gnomad4 NFE exome AF: 0.0370

Gnomad4 OTH exome AF: 0.0382

GnomAD4 genome AF: 0.00697 AC: 1036 AN: 148538 Hom.: 9 Cov.: 32 AF XY: 0.00698 AC XY: 505 AN XY: 72342

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.00235

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00787

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.000303

Gnomad4 NFE AF: 0.000210

Gnomad4 OTH AF: 0.00537

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs149170192; hg19: chr15-78397503;