chr16-85105567-G-T

Position:

• chr16-85105567-G-T

Variant summary

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

The NM_198491.3(CIBAR2):​c.433-136C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 636,618 control chromosomes in the GnomAD database, including 110,610 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 0.64 (32414 hom., cov: 32)
  • Exomes 𝑓: 0.56 (78196 hom.)
• Consequence: CIBAR2 NM_198491.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

CIBAR2 (HGNC:24781): (CBY1 interacting BAR domain containing 2) Predicted to be involved in cilium assembly. Predicted to be located in centriole and cytoplasm. Predicted to be active in ciliary basal body and ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIBAR2	NM_198491.3	c.433-136C>A		intron_variant		ENST00000539556.6	NP_940893.1
CIBAR2	NM_001366920.1	c.433-136C>A		intron_variant			NP_001353849.1
CIBAR2	XM_011523063.2	c.433-136C>A		intron_variant			XP_011521365.1
CIBAR2	XM_017023198.2	c.433-136C>A		intron_variant			XP_016878687.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CIBAR2	ENST00000539556.6	c.433-136C>A		intron_variant		5	NM_198491.3	ENSP00000443411.1
CIBAR2	ENST00000618669.3	c.148-136C>A		intron_variant		5		ENSP00000478373.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96609 AN: 151970 Hom.: 32366 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.642

GnomAD4 exome AF: 0.558 AC: 270406 AN: 484530 Hom.: 78196 AF XY: 0.562 AC XY: 142792 AN XY: 254214

Gnomad4 AFR exome AF: 0.863

Gnomad4 AMR exome AF: 0.495

Gnomad4 ASJ exome AF: 0.589

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.609

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.568

Gnomad4 OTH exome AF: 0.586

GnomAD4 genome AF: 0.636 AC: 96706 AN: 152088 Hom.: 32414 Cov.: 32 AF XY: 0.629 AC XY: 46728 AN XY: 74348

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.644

Alfa AF: 0.584 Hom.: 35062

Bravo AF: 0.649

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.058
DANN	Benign	0.73

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: rs8050910; hg19: chr16-85139173; COSMIC: COSV73320585;