4-24805665-C-T

Position:

• chr4-24805665-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395273.1(CCDC149):​c.*2724G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,260 control chromosomes in the GnomAD database, including 65,126 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 0.92 (65126 hom., cov: 32)
• Consequence: CCDC149 NM_001395273.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC149	NM_001395273.1	c.*2724G>A		3_prime_UTR_variant	13/13	ENST00000635206.3	NP_001382202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC149	ENST00000635206	c.*2724G>A		3_prime_UTR_variant	13/13	5	NM_001395273.1	ENSP00000488929.2

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140687 AN: 152142 Hom.: 65073 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.925 AC: 140797 AN: 152260 Hom.: 65126 Cov.: 32 AF XY: 0.926 AC XY: 68967 AN XY: 74444

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.913

Alfa AF: 0.922 Hom.: 85081

Bravo AF: 0.925

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs758946; hg19: chr4-24807287;