rs3114316

chr7-77253605-C-T

Variant summary

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

The NM_020879.3(CCDC146):c.450-901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,116 control chromosomes in the GnomAD database, including 43,052 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 0.74 (43052 hom., cov: 33)
• Consequence: CCDC146 NM_020879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

CCDC146 (HGNC:29296): (coiled-coil domain containing 146) Located in centriole. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC146	NM_020879.3	c.450-901C>T		intron_variant		ENST00000285871.5
LOC102723791	XR_927688.3	n.513-728G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC146	ENST00000285871.5	c.450-901C>T		intron_variant		1	NM_020879.3	P1
	ENST00000476561.2	n.422+1721G>A		intron_variant, non_coding_transcript_variant		4
CCDC146	ENST00000415750.5	c.450-901C>T		intron_variant		4
CCDC146	ENST00000461882.1	n.86-901C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112082 AN: 151998 Hom.: 43038 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.737 AC: 112145 AN: 152116 Hom.: 43052 Cov.: 33 AF XY: 0.732 AC XY: 54396 AN XY: 74356

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.759

Alfa AF: 0.781 Hom.: 8270

Bravo AF: 0.722

Asia WGS AF: 0.696 AC: 2421 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	3.4
Dann	Benign	0.49

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: rs3114316; hg19: chr7-76882922;