chr9-15986718-T-C

Variant names:

• chr9-15986718-T-C
• rs1927702
• ENST00000486641.2:n.369-33871T>C

Variant summary

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

The ENST00000486641.2(CCDC171):​n.369-33871T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,998 control chromosomes in the GnomAD database, including 20,027 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 0.50 (20027 hom., cov: 32)
• Consequence: CCDC171 ENST00000486641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 18 publications found

Genes affected

CCDC171 (HGNC:29828): (coiled-coil domain containing 171)

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 (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486641.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC171	ENST00000486641.2	TSL:1	n.369-33871T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75137 AN: 151878 Hom.: 19977 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.495 AC: 75250 AN: 151998 Hom.: 20027 Cov.: 32 AF XY: 0.486 AC XY: 36124 AN XY: 74304

African (AFR) AF: 0.705 AC: 29232 AN: 41458

American (AMR) AF: 0.380 AC: 5801 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1300 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1758 AN: 5168

South Asian (SAS) AF: 0.519 AC: 2502 AN: 4824

European-Finnish (FIN) AF: 0.350 AC: 3694 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29339 AN: 67948

Other (OTH) AF: 0.443 AC: 937 AN: 2116

Alfa AF: 0.466 Hom.: 27093

Bravo AF: 0.501

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs1927702; hg19: chr9-15986716;