rs10209732

Positions:

• chr2-158249747-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC148	NM_138803.4	c.1251+1025T>C		intron_variant		ENST00000283233.10	NP_620158.3
CCDC148	NM_001301684.2	c.813+1025T>C		intron_variant			NP_001288613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC148	ENST00000283233.10	c.1251+1025T>C		intron_variant		1	NM_138803.4	ENSP00000283233

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

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.199

Alfa AF: 0.210 Hom.: 3532

Bravo AF: 0.163

Asia WGS AF: 0.123 AC: 429 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs10209732; hg19: chr2-159106259;