16-85105567-G-T

Variant names:

• chr16-85105567-G-T
• rs8050910
• NM_198491.3:c.433-136C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CIBAR2	NM_198491.3	c.433-136C>A		intron_variant	Intron 5 of 8	ENST00000539556.6	NP_940893.1
CIBAR2	NM_001366920.1	c.433-136C>A		intron_variant	Intron 5 of 8		NP_001353849.1
CIBAR2	XM_011523063.2	c.433-136C>A		intron_variant	Intron 5 of 9		XP_011521365.1
CIBAR2	XM_017023198.2	c.433-136C>A		intron_variant	Intron 5 of 9		XP_016878687.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIBAR2	ENST00000539556.6	c.433-136C>A		intron_variant	Intron 5 of 8	5	NM_198491.3	ENSP00000443411.1
CIBAR2	ENST00000618669.3	c.148-136C>A		intron_variant	Intron 3 of 6	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

African (AFR) AF: 0.863 AC: 11892 AN: 13786

American (AMR) AF: 0.495 AC: 10958 AN: 22152

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 8389 AN: 14232

East Asian (EAS) AF: 0.321 AC: 9966 AN: 31086

South Asian (SAS) AF: 0.609 AC: 28861 AN: 47364

European-Finnish (FIN) AF: 0.483 AC: 15026 AN: 31098

Middle Eastern (MID) AF: 0.654 AC: 2359 AN: 3606

European-Non Finnish (NFE) AF: 0.568 AC: 167173 AN: 294258

Other (OTH) AF: 0.586 AC: 15782 AN: 26948

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

African (AFR) AF: 0.866 AC: 35951 AN: 41518

American (AMR) AF: 0.540 AC: 8254 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2035 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1743 AN: 5164

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4820

European-Finnish (FIN) AF: 0.469 AC: 4950 AN: 10564

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38796 AN: 67964

Other (OTH) AF: 0.644 AC: 1359 AN: 2110

Alfa AF: 0.604 Hom.: 58557

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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