chr7-77239090-A-G

Position:

• chr7-77239090-A-G

Variant summary

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

The NM_020879.3(CCDC146):​c.239+2061A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 152,242 control chromosomes in the GnomAD database, including 488 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 0.051 (488 hom., cov: 32)
• Consequence: CCDC146 NM_020879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

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

LOC105375359 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC146	NM_020879.3	c.239+2061A>G		intron_variant		ENST00000285871.5	NP_065930.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC146	ENST00000285871.5	c.239+2061A>G		intron_variant		1	NM_020879.3	ENSP00000285871.4
CCDC146	ENST00000415750.5	c.239+2061A>G		intron_variant		4		ENSP00000388649.1

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7749 AN: 152124 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00573

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0510 AC: 7764 AN: 152242 Hom.: 488 Cov.: 32 AF XY: 0.0499 AC XY: 3713 AN XY: 74436

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0236

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.0385

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00573

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0343 Hom.: 43

Bravo AF: 0.0585

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.48

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: rs10499830; hg19: chr7-76868407;