chr4-24805665-C-T

Variant names:

• chr4-24805665-C-T
• rs758946
• NM_001395273.1:c.*2724G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395273.1. 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
	CCDC149	NM_001395273.1	MANE Select	c.*2724G>A		3_prime_UTR	Exon 13 of 13	NP_001382202.1	A0A0U1RQD2
	CCDC149	NM_001130726.5		c.*2724G>A		3_prime_UTR	Exon 12 of 12	NP_001124198.2	A0A8V8PSJ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC149	ENST00000635206.3	TSL:5 MANE Select	c.*2724G>A		3_prime_UTR	Exon 13 of 13	ENSP00000488929.2	A0A0U1RQD2

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

African (AFR) AF: 0.923 AC: 38357 AN: 41536

American (AMR) AF: 0.935 AC: 14315 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3098 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4785 AN: 5170

South Asian (SAS) AF: 0.921 AC: 4438 AN: 4818

European-Finnish (FIN) AF: 0.946 AC: 10033 AN: 10610

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62777 AN: 68026

Other (OTH) AF: 0.913 AC: 1932 AN: 2116

Alfa AF: 0.923 Hom.: 193924

Bravo AF: 0.925

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs758946; hg19: chr4-24807287;