NM_001395273.1:c.358-4942T>C

Variant names:

• chr4-24843214-A-G
• rs10489030
• NM_001395273.1:c.358-4942T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395273.1(CCDC149):​c.358-4942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,230 control chromosomes in the GnomAD database, including 1,041 homozygotes. 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: 𝑓 0.11 (1041 hom., cov: 32)
• Consequence: CCDC149 NM_001395273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770
• Publications: 4 publications found

Genes affected

CCDC149 (HGNC:25405): (coiled-coil domain containing 149)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC149	NM_001395273.1	c.358-4942T>C		intron_variant	Intron 4 of 12	ENST00000635206.3	NP_001382202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC149	ENST00000635206.3	c.358-4942T>C		intron_variant	Intron 4 of 12	5	NM_001395273.1	ENSP00000488929.2

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16434 AN: 152112 Hom.: 1041 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.108 AC: 16456 AN: 152230 Hom.: 1041 Cov.: 32 AF XY: 0.107 AC XY: 7934 AN XY: 74432

African (AFR) AF: 0.182 AC: 7537 AN: 41526

American (AMR) AF: 0.0737 AC: 1127 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0925 AC: 446 AN: 4822

European-Finnish (FIN) AF: 0.0619 AC: 656 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 6006 AN: 68008

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0818 Hom.: 547

Bravo AF: 0.113

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.60
PhyloP100		0.77
Mutation Taster		=100/0	polymorphism (auto)

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: rs10489030; hg19: chr4-24844836;