rs916213

Positions:

• chr22-37001509-T-A
• chr22-37001509-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001163857.2(CIMIP4):​c.489+328A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: CIMIP4 NM_001163857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

CIMIP4 (HGNC:28568): (ciliary microtubule inner protein 4)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIMIP4	NM_001163857.2	c.489+328A>T		intron_variant		ENST00000381821.2	NP_001157329.1
CIMIP4	NM_178552.4	c.234+328A>T		intron_variant			NP_848647.1
CIMIP4	XM_011530165.3	c.489+328A>T		intron_variant			XP_011528467.1
CIMIP4	XM_011530166.2	c.234+328A>T		intron_variant			XP_011528468.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX33	ENST00000381821.2	c.489+328A>T		intron_variant		1	NM_001163857.2	ENSP00000371243.1
TEX33	ENST00000402860.7	c.234+328A>T		intron_variant		1		ENSP00000385179.3
TEX33	ENST00000405091.6	c.489+328A>T		intron_variant		5		ENSP00000386118.2
TEX33	ENST00000442538.5	c.63+684A>T		intron_variant		3		ENSP00000406640.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.51

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: rs916213; hg19: chr22-37397550;