17-20895806-A-T

Variant names:

• chr17-20895806-A-T
• rs2279263
• ENST00000327925.7:n.358T>A

Variant summary

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

The ENST00000327925.7(CCDC144NL):​n.358T>A variant causes a non coding transcript exon 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: CCDC144NL ENST00000327925.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 14 publications found

Genes affected

CCDC144NL (HGNC:):

CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)

CCDC144NL (HGNC:33735): (CCDC144A N-terminal like (pseudogene))

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 (MetaRNN=0.04915923).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000327925.7. 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
	CCDC144NL	NR_164128.1		n.358T>A		non_coding_transcript_exon	Exon 1 of 4
	CCDC144NL-AS1	NR_104185.2		n.362+3374A>T		intron	N/A
	CCDC144NL-AS1	NR_160710.1		n.620+3374A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC144NL	ENST00000327925.7	TSL:1	n.358T>A		non_coding_transcript_exon	Exon 1 of 4
	CCDC144NL-AS1	ENST00000583962.3	TSL:1	n.424+3374A>T		intron	N/A
	CCDC144NL	ENST00000647562.3		n.215T>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 63

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.7
DANN	Benign	0.82
DEOGEN2	Benign	0.0012	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0053	N
LIST_S2	Benign	0.32	T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.049	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.38
PrimateAI	Uncertain	0.51	T
Polyphen		0.27	B
MutPred		0.44		Loss of stability (P = 0.0175)
ClinPred		0.081	T
GERP RS		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.062
gMVP		0.030

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: rs2279263; hg19: chr17-20799119;