rs2914941

Variant names:

• chr8-93716983-C-G
• rs2914941
• NM_145269.5:c.544-1692C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-93716983-C-G
• chr8-93716983-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145269.5(CIBAR1):​c.544-1692C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,048 control chromosomes in the GnomAD database, including 30,272 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 0.62 (30272 hom., cov: 32)
• Consequence: CIBAR1 NM_145269.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 2 publications found

Genes affected

CIBAR1 (HGNC:30452): (CBY1 interacting BAR domain containing 1) Enables phospholipid binding activity. Involved in several processes, including inner mitochondrial membrane organization; limb morphogenesis; and membrane tubulation. Located in several cellular components, including centriole; ciliary base; and mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]

CIBAR1 Gene-Disease associations (from GenCC):

• postaxial polydactyly type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• polydactyly, postaxial, type A9

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIBAR1	NM_145269.5	c.544-1692C>G		intron_variant	Intron 6 of 8	ENST00000518322.6	NP_660312.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIBAR1	ENST00000518322.6	c.544-1692C>G		intron_variant	Intron 6 of 8	5	NM_145269.5	ENSP00000429367.1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94704 AN: 151930 Hom.: 30250 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.623 AC: 94758 AN: 152048 Hom.: 30272 Cov.: 32 AF XY: 0.623 AC XY: 46301 AN XY: 74328

African (AFR) AF: 0.495 AC: 20502 AN: 41438

American (AMR) AF: 0.578 AC: 8837 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2278 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5164

South Asian (SAS) AF: 0.717 AC: 3457 AN: 4822

European-Finnish (FIN) AF: 0.687 AC: 7247 AN: 10556

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.701 AC: 47678 AN: 67994

Other (OTH) AF: 0.647 AC: 1367 AN: 2114

Alfa AF: 0.653 Hom.: 3898

Bravo AF: 0.607

Asia WGS AF: 0.581 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.51
PhyloP100		0.0
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: rs2914941; hg19: chr8-94729211;