2-196715003-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC150	NM_001080539.2	c.1866+2264T>C		intron_variant		ENST00000389175.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC150	ENST00000389175.9	c.1866+2264T>C		intron_variant		5	NM_001080539.2	A2

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.574

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	9.5
Dann	Benign	0.50

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: rs12997060; hg19: chr2-197579727;