rs1927702

chr9-15986718-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486641.2(CCDC171):n.369-33871T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC171	XM_017014432.3	c.3870-31585T>C		intron_variant
CCDC171	XM_017014437.3	c.3778-35614T>C		intron_variant
CCDC171	XR_001746227.3	n.4149-49375T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC171	ENST00000486641.2	n.369-33871T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.443

Alfa AF: 0.448 Hom.: 11785

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927702; hg19: chr9-15986716;