rs1533802

Variant names:

• chr2-26570247-A-C
• rs1533802
• NM_001105519.3:c.75-5655A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-26570247-A-C
• chr2-26570247-A-G

Variant summary

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

The NM_001105519.3(CIMIP2C):​c.75-5655A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,066 control chromosomes in the GnomAD database, including 35,043 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 0.66 (35043 hom., cov: 33)
• Consequence: CIMIP2C NM_001105519.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 3 publications found

Genes affected

CIMIP2C (HGNC:27938): (ciliary microtubule inner protein 2C) Located in nucleus. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMIP2C	NM_001105519.3	c.75-5655A>C		intron_variant	Intron 1 of 3	ENST00000329615.4	NP_001098989.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIMIP2C	ENST00000329615.4	c.75-5655A>C		intron_variant	Intron 1 of 3	5	NM_001105519.3	ENSP00000332875.3
CIMIP2C	ENST00000409392.5	c.1-1869A>C		intron_variant	Intron 1 of 4	3		ENSP00000386615.1
CIMIP2C	ENST00000479453.1	n.76-5655A>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100840 AN: 151948 Hom.: 35022 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.663 AC: 100892 AN: 152066 Hom.: 35043 Cov.: 33 AF XY: 0.670 AC XY: 49859 AN XY: 74368

African (AFR) AF: 0.436 AC: 18074 AN: 41444

American (AMR) AF: 0.769 AC: 11762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2454 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3847 AN: 5162

South Asian (SAS) AF: 0.718 AC: 3456 AN: 4816

European-Finnish (FIN) AF: 0.795 AC: 8427 AN: 10594

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50655 AN: 67980

Other (OTH) AF: 0.694 AC: 1465 AN: 2112

Alfa AF: 0.705 Hom.: 6115

Bravo AF: 0.651

Asia WGS AF: 0.733 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.69
PhyloP100		-0.038
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: rs1533802; hg19: chr2-26793115;