chr7-77136737-A-G

Variant names:

• chr7-77136737-A-G
• rs2539149
• NM_020879.3:c.-12+14005A>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020879.3(CCDC146):​c.-12+14005A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00025 (0 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: CCDC146 NM_020879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

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

ENSG00000259628 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC146	NM_020879.3	c.-12+14005A>G		intron_variant	Intron 1 of 18	ENST00000285871.5	NP_065930.2
CCDC146	XM_047420662.1	c.-141+14005A>G		intron_variant	Intron 1 of 19		XP_047276618.1
CCDC146	XM_047420664.1	c.-10+14005A>G		intron_variant	Intron 1 of 17		XP_047276620.1
LOC124901678	XR_007060391.1	n.847-8011T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC146	ENST00000285871.5	c.-12+14005A>G		intron_variant	Intron 1 of 18	1	NM_020879.3	ENSP00000285871.4
CCDC146	ENST00000415750.5	c.-12+14269A>G		intron_variant	Intron 1 of 4	4		ENSP00000388649.1
ENSG00000259628	ENST00000459742.1	n.59-30921A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33 AN: 136514 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.000434

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000617

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000203

Gnomad SAS AF: 0.000688

Gnomad FIN AF: 0.000107

Gnomad MID AF: 0.00368

Gnomad NFE AF: 0.0000484

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000249 AC: 34 AN: 136596 Hom.: 0 Cov.: 31 AF XY: 0.000211 AC XY: 14 AN XY: 66360

Gnomad4 AFR AF: 0.000460

Gnomad4 AMR AF: 0.000616

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000204

Gnomad4 SAS AF: 0.000689

Gnomad4 FIN AF: 0.000107

Gnomad4 NFE AF: 0.0000484

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00637 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.97

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: rs2539149; hg19: chr7-76766054;