rs10209732

Variant names:

• chr2-158249747-A-G
• rs10209732
• NM_138803.4:c.1251+1025T>C

Variant summary

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

The NM_138803.4(CCDC148):​c.1251+1025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,074 control chromosomes in the GnomAD database, including 2,646 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 0.16 (2646 hom., cov: 32)
• Consequence: CCDC148 NM_138803.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.940
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 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.1251+1025T>C		intron	N/A	NP_620158.3
	CCDC148	NM_001301684.2		c.813+1025T>C		intron	N/A	NP_001288613.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC148	ENST00000283233.10	TSL:1 MANE Select	c.1251+1025T>C		intron	N/A	ENSP00000283233.5	Q8NFR7-1
	CCDC148	ENST00000448656.5	TSL:1	n.*842+1025T>C		intron	N/A	ENSP00000415540.1	F8WCV9
	CCDC148	ENST00000409187.5	TSL:5	c.1278+1025T>C		intron	N/A	ENSP00000386674.1	B8ZZV3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25048 AN: 151956 Hom.: 2647 Cov.: 32

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.165 AC: 25060 AN: 152074 Hom.: 2646 Cov.: 32 AF XY: 0.164 AC XY: 12181 AN XY: 74330

African (AFR) AF: 0.0459 AC: 1906 AN: 41540

American (AMR) AF: 0.235 AC: 3589 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3468

East Asian (EAS) AF: 0.136 AC: 705 AN: 5168

South Asian (SAS) AF: 0.0500 AC: 241 AN: 4822

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10574

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14902 AN: 67940

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.202 Hom.: 4928

Bravo AF: 0.163

Asia WGS AF: 0.123 AC: 429 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		0.94
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10209732;

hg19: chr2-159106259;