rs3797310

Variant names:

• chr5-42756838-C-G
• rs3797310
• NM_001134848.2:c.-50C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-42756838-C-G
• chr5-42756838-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001134848.2(CCDC152):​c.-50C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CCDC152 NM_001134848.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 18 publications found

Genes affected

CCDC152 (HGNC:34438): (coiled-coil domain containing 152)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134848.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC152	NM_001134848.2	MANE Select	c.-50C>G		5_prime_UTR	Exon 1 of 9	NP_001128320.1	Q4G0S7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC152	ENST00000361970.10	TSL:1 MANE Select	c.-50C>G		5_prime_UTR	Exon 1 of 9	ENSP00000354888.5	Q4G0S7-1
	CCDC152	ENST00000927601.1		c.-294C>G		5_prime_UTR	Exon 1 of 10	ENSP00000597660.1
	CCDC152	ENST00000927600.1		c.-50C>G		5_prime_UTR	Exon 1 of 8	ENSP00000597659.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.89
PromoterAI		0.26	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3797310; hg19: chr5-42756940;