ENST00000486641.2:n.369-33871T>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC171	XM_017014432.3	c.3870-31585T>C		intron_variant	Intron 26 of 26		XP_016869921.1
CCDC171	XM_017014437.3	c.3778-35614T>C		intron_variant	Intron 25 of 25		XP_016869926.1
CCDC171	XR_001746227.3	n.4149-49375T>C		intron_variant	Intron 25 of 27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000486641.2	n.369-33871T>C		intron_variant	Intron 3 of 9	1

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 v4.3

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;