2-196715003-T-C

Variant names:

• chr2-196715003-T-C
• rs12997060
• NM_001080539.2:c.1866+2264T>C

Variant summary

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

The NM_001080539.2(CCDC150):​c.1866+2264T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,062 control chromosomes in the GnomAD database, including 27,577 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 0.54 (27577 hom., cov: 31)
• Consequence: CCDC150 NM_001080539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 1 publications found

Genes affected

CCDC150 (HGNC:26834): (coiled-coil domain containing 150)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080539.2. 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
	CCDC150	NM_001080539.2	MANE Select	c.1866+2264T>C		intron	N/A	NP_001074008.1
	CCDC150	NM_001412753.1		c.1689+2751T>C		intron	N/A	NP_001399682.1
	CCDC150	NM_001353339.2		c.807+2751T>C		intron	N/A	NP_001340268.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC150	ENST00000389175.9	TSL:5 MANE Select	c.1866+2264T>C		intron	N/A	ENSP00000373827.4
	CCDC150	ENST00000448409.5	TSL:1	n.327+1320T>C		intron	N/A	ENSP00000413957.1
	CCDC150	ENST00000409270.5	TSL:5	c.327+1320T>C		intron	N/A	ENSP00000387257.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82519 AN: 151944 Hom.: 27575 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.543 AC: 82523 AN: 152062 Hom.: 27577 Cov.: 31 AF XY: 0.552 AC XY: 41036 AN XY: 74326

African (AFR) AF: 0.133 AC: 5506 AN: 41512

American (AMR) AF: 0.709 AC: 10837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2302 AN: 3466

East Asian (EAS) AF: 0.920 AC: 4762 AN: 5176

South Asian (SAS) AF: 0.672 AC: 3234 AN: 4816

European-Finnish (FIN) AF: 0.742 AC: 7833 AN: 10558

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46134 AN: 67948

Other (OTH) AF: 0.574 AC: 1207 AN: 2104

Alfa AF: 0.596 Hom.: 3772

Bravo AF: 0.524

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.5
DANN	Benign	0.50
PhyloP100		0.080
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

Other links and lift over

dbSNP: rs12997060; hg19: chr2-197579727;