22-37001509-T-C

Position:

• chr22-37001509-T-C

Variant summary

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

The NM_001163857.2(CIMIP4):​c.489+328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,962 control chromosomes in the GnomAD database, including 33,214 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 0.65 (33214 hom., 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99155 AN: 151844 Hom.: 33172 Cov.: 30

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.653 AC: 99259 AN: 151962 Hom.: 33214 Cov.: 30 AF XY: 0.651 AC XY: 48344 AN XY: 74260

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.675

Alfa AF: 0.608 Hom.: 13636

Bravo AF: 0.677

Asia WGS AF: 0.608 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.30

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;