rs3800560

Variant names:

• chr7-128821040-C-A
• rs3800560
• NM_022742.5:c.*6-759C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-128821040-C-A
• chr7-128821040-C-T

Variant summary

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

The NM_022742.5(CCDC136):​c.*6-759C>A variant causes a intron 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: CCDC136 NM_022742.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 4 publications found

Genes affected

CCDC136 (HGNC:22225): (coiled-coil domain containing 136) Predicted to be involved in acrosome assembly and single fertilization. Predicted to be integral component of membrane. Predicted to be active in acrosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022742.5. 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
	CCDC136	NM_022742.5	MANE Select	c.*6-759C>A		intron	N/A	NP_073579.5
	CCDC136	NM_001367764.1		c.3514-759C>A		intron	N/A	NP_001354693.1
	CCDC136	NM_001363423.2		c.2914-759C>A		intron	N/A	NP_001350352.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC136	ENST00000297788.9	TSL:1 MANE Select	c.*6-759C>A		intron	N/A	ENSP00000297788.4	Q96JN2-1
	CCDC136	ENST00000494552.5	TSL:1	c.2992-759C>A		intron	N/A	ENSP00000417931.1	H7C4R2
	CCDC136	ENST00000961328.1		c.*6-759C>A		intron	N/A	ENSP00000631387.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		-0.28

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

Other links and lift over

dbSNP: rs3800560; hg19: chr7-128461094;