rs561026830

Variant names:

• chr17-16690692-C-A
• rs561026830
• NM_001382000.1:c.292C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-16690692-C-A
• chr17-16690692-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001382000.1(CCDC144A):​c.292C>A​(p.His98Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC144A NM_001382000.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0460
• Publications: 0 publications found

Genes affected

CCDC144A (HGNC:29072): (coiled-coil domain containing 144A)

ENSG00000266302 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0866344).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382000.1. 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
	CCDC144A	NM_001382000.1	MANE Select	c.292C>A	p.His98Asn	missense	Exon 1 of 17	NP_001368929.1	C9JT67
	CCDC144A	NM_014695.3		c.292C>A	p.His98Asn	missense	Exon 1 of 18	NP_055510.1	A2RUR9-1
	CCDC144A	NR_130142.2		n.452C>A		non_coding_transcript_exon	Exon 1 of 16

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC144A	ENST00000399273.5	TSL:1 MANE Select	c.292C>A	p.His98Asn	missense	Exon 1 of 17	ENSP00000382215.1	C9JT67
	CCDC144A	ENST00000360524.12	TSL:1	c.292C>A	p.His98Asn	missense	Exon 1 of 18	ENSP00000353717.8	A2RUR9-1
	CCDC144A	ENST00000360495.9	TSL:1	n.292C>A		non_coding_transcript_exon	Exon 1 of 16	ENSP00000353685.5	A6NG92

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152214 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000482

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000205 AC: 3 AN: 1461402 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 726984

African (AFR) AF: 0.00 AC: 0 AN: 33472

American (AMR) AF: 0.00 AC: 0 AN: 44696

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26116

East Asian (EAS) AF: 0.00 AC: 0 AN: 39684

South Asian (SAS) AF: 0.00 AC: 0 AN: 86222

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53396

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5746

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111704

Other (OTH) AF: 0.0000166 AC: 1 AN: 60366

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152214 Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2 AN XY: 74360

African (AFR) AF: 0.0000482 AC: 2 AN: 41460

American (AMR) AF: 0.00 AC: 0 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68046

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.64
DANN	Benign	0.57
DEOGEN2	Benign	0.0051	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0021	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.087	T
MetaSVM	Benign	-0.97	T
PhyloP100		0.046
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.20	N
REVEL	Benign	0.023
Sift	Benign	0.20	T
Sift4G	Uncertain	0.043	D
Polyphen		0.0030	B
Vest4		0.28
MutPred		0.34		Gain of sheet (P = 0.0827)
MVP		0.030
ClinPred		0.059	T
GERP RS		0.54
PromoterAI		0.012	Neutral
Varity_R		0.084
gMVP		0.028
Mutation Taster		=99/1	polymorphism

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: rs561026830; hg19: chr17-16594006;