2-158391218-C-T

Variant names:

• chr2-158391218-C-T
• rs2251471
• NM_138803.4:c.26-32648G>A

Variant summary

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

The NM_138803.4(CCDC148):​c.26-32648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,148 control chromosomes in the GnomAD database, including 59,671 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 0.88 (59671 hom., cov: 32)
• Consequence: CCDC148 NM_138803.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 4 publications found

Genes affected

CCDC148 (HGNC:25191): (coiled-coil domain containing 148)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138803.4. 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
	CCDC148	NM_138803.4	MANE Select	c.26-32648G>A		intron	N/A	NP_620158.3
	CCDC148	NM_001301684.2		c.-157-32648G>A		intron	N/A	NP_001288613.1
	CCDC148	NM_001301685.2		c.26-32648G>A		intron	N/A	NP_001288614.1	Q8NFR7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC148	ENST00000283233.10	TSL:1 MANE Select	c.26-32648G>A		intron	N/A	ENSP00000283233.5	Q8NFR7-1
	CCDC148	ENST00000409889.1	TSL:1	c.26-32648G>A		intron	N/A	ENSP00000386583.1	Q8NFR7-3
	CCDC148	ENST00000417066.5	TSL:1	n.26-50538G>A		intron	N/A	ENSP00000400751.1	F8WC92

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134057 AN: 152030 Hom.: 59651 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.882 AC: 134123 AN: 152148 Hom.: 59671 Cov.: 32 AF XY: 0.882 AC XY: 65591 AN XY: 74374

African (AFR) AF: 0.746 AC: 30974 AN: 41502

American (AMR) AF: 0.931 AC: 14210 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2892 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4337 AN: 5158

South Asian (SAS) AF: 0.940 AC: 4530 AN: 4818

European-Finnish (FIN) AF: 0.936 AC: 9933 AN: 10610

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

European-Non Finnish (NFE) AF: 0.946 AC: 64308 AN: 68010

Other (OTH) AF: 0.883 AC: 1861 AN: 2108

Alfa AF: 0.926 Hom.: 54683

Bravo AF: 0.873

Asia WGS AF: 0.885 AC: 3077 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.57
PhyloP100		-0.11
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: rs2251471; hg19: chr2-159247730;