chr3-14655314-GA-G

Position:

• chr3-14655314-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016474.5(CCDC174):​c.148-203delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 141,996 control chromosomes in the GnomAD database, including 313 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.045 (313 hom., cov: 31)
• Consequence: CCDC174 NM_016474.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.150

Genes affected

CCDC174 (HGNC:28033): (coiled-coil domain containing 174) The protein encoded by this gene is found in the nucleus, where it interacts with eukaryotic translation initiation factor 4A, isoform 3. The encoded protein appears to be a part of the exon junction complex, which is involved in RNA processing, translation, and nonsense-mediated mRNA decay. A mutation in this gene has been associated with infantile hypotonia with psychomotor retardation. [provided by RefSeq, Mar 2016]

CCDC174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-14655314-GA-G is Benign according to our data. Variant chr3-14655314-GA-G is described in ClinVar as [Benign]. Clinvar id is 1253075.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC174	NM_016474.5	c.148-203delA		intron_variant		ENST00000383794.7	NP_057558.3
CCDC174	NM_001410719.1	c.148-203delA		intron_variant			NP_001397648.1
CCDC174	XM_017006555.3	c.148-203delA		intron_variant			XP_016862044.1
CCDC174	NR_135523.2	n.223-203delA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC174	ENST00000383794.7	c.148-203delA		intron_variant		1	NM_016474.5	ENSP00000373304.3
CCDC174	ENST00000465759.1	n.212-203delA		intron_variant		1
CCDC174	ENST00000303688.8	c.148-203delA		intron_variant		5		ENSP00000302344.7
CCDC174	ENST00000463438.5	n.221-203delA		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6396 AN: 141928 Hom.: 310 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00229

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.00141

Gnomad SAS AF: 0.00510

Gnomad FIN AF: 0.00524

Gnomad MID AF: 0.0392

Gnomad NFE AF: 0.00859

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0452 AC: 6418 AN: 141996 Hom.: 313 Cov.: 31 AF XY: 0.0440 AC XY: 3023 AN XY: 68636

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.00141

Gnomad4 SAS AF: 0.00490

Gnomad4 FIN AF: 0.00524

Gnomad4 NFE AF: 0.00860

Gnomad4 OTH AF: 0.0318

Bravo AF: 0.0477

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs113359021; hg19: chr3-14696821;