19-472149-C-T

Variant summary

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

The NM_182577.3(ODF3L2):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: ODF3L2 NM_182577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

Genes affected

ODF3L2 (HGNC:):

CIMAP1D (HGNC:26841): (CIMAP1 family member D) Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODF3L2	NM_182577.3	c.235+245G>A		intron_variant		ENST00000315489.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIMAP1D	ENST00000315489.5	c.235+245G>A		intron_variant		1	NM_182577.3	P2
CIMAP1D	ENST00000382696.7	c.127+2472G>A		intron_variant		1		A2
CIMAP1D	ENST00000591681.3	n.222+245G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.739

Alfa AF: 0.777 Hom.: 24277

Bravo AF: 0.754

Asia WGS AF: 0.712 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
Dann	Benign	0.20

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: rs2392794; hg19: chr19-472149;