chr22-50530129-C-T

Position:

• chr22-50530129-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000468249.1(CIMAP1B):​n.1303G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 373,196 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.028 (167 hom., cov: 33)
  • Exomes 𝑓: 0.0047 (38 hom.)
• Consequence: CIMAP1B ENST00000468249.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.33

Genes affected

CIMAP1B (HGNC:34388): (ciliary microtubule associated protein 1B) Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

TYMP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 22-50530129-C-T is Benign according to our data. Variant chr22-50530129-C-T is described in ClinVar as [Benign]. Clinvar id is 1225979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TYMP	NM_001257988.1			upstream_gene_variant
TYMP	NM_001257989.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIMAP1B	ENST00000468249.1	n.1303G>A		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.0278 AC: 4225 AN: 152012 Hom.: 167 Cov.: 33

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.000677

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.00468 AC: 1034 AN: 221076 Hom.: 38 Cov.: 0 AF XY: 0.00427 AC XY: 481 AN XY: 112540

Gnomad4 AFR exome AF: 0.0974

Gnomad4 AMR exome AF: 0.0121

Gnomad4 ASJ exome AF: 0.00864

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000755

Gnomad4 OTH exome AF: 0.0115

GnomAD4 genome AF: 0.0278 AC: 4228 AN: 152120 Hom.: 167 Cov.: 33 AF XY: 0.0274 AC XY: 2039 AN XY: 74390

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000677

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0233 Hom.: 17

Bravo AF: 0.0314

Asia WGS AF: 0.00640 AC: 22 AN: 3452

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.81
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs141083282; hg19: chr22-50968558;