19-472149-C-T

Variant names:

• chr19-472149-C-T
• rs2392794
• NM_182577.3:c.235+245G>A

Variant summary

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

The NM_182577.3(CIMAP1D):​c.235+245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,112 control chromosomes in the GnomAD database, including 44,110 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 0.76 (44110 hom., cov: 33)
• Consequence: CIMAP1D NM_182577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 9 publications found

Genes affected

CIMAP1D (HGNC:26841): (CIMAP1 family member D) Located in cytoplasmic microtubule. [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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182577.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMAP1D	NM_182577.3	MANE Select	c.235+245G>A		intron	N/A	NP_872383.1	Q3SX64-1
	CIMAP1D	NM_001385597.1		c.127+2472G>A		intron	N/A	NP_001372526.1	Q3SX64-2
	CIMAP1D	NM_001385598.1		c.-89-4387G>A		intron	N/A	NP_001372527.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMAP1D	ENST00000315489.5	TSL:1 MANE Select	c.235+245G>A		intron	N/A	ENSP00000318029.2	Q3SX64-1
	CIMAP1D	ENST00000382696.7	TSL:1	c.127+2472G>A		intron	N/A	ENSP00000372143.2	Q3SX64-2
	CIMAP1D	ENST00000591681.3	TSL:2	n.222+245G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115517 AN: 151994 Hom.: 44069 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.760 AC: 115614 AN: 152112 Hom.: 44110 Cov.: 33 AF XY: 0.763 AC XY: 56745 AN XY: 74350

African (AFR) AF: 0.685 AC: 28432 AN: 41484

American (AMR) AF: 0.804 AC: 12283 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3468

East Asian (EAS) AF: 0.789 AC: 4075 AN: 5166

South Asian (SAS) AF: 0.713 AC: 3437 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8659 AN: 10592

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53875 AN: 67980

Other (OTH) AF: 0.739 AC: 1563 AN: 2114

Alfa AF: 0.775 Hom.: 34254

Bravo AF: 0.754

Asia WGS AF: 0.712 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		-0.38
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: rs2392794; hg19: chr19-472149;