9-16034540-G-T

Variant names:

• chr9-16034540-G-T
• rs3008706
• ENST00000486641.2:n.999-917G>T

Variant summary

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

The ENST00000486641.2(CCDC171):​n.999-917G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,106 control chromosomes in the GnomAD database, including 1,792 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 0.15 (1792 hom., cov: 32)
• Consequence: CCDC171 ENST00000486641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC171	XR_001746227.3	n.4149-1553G>T		intron_variant	Intron 25 of 27
CCDC171	XR_007061261.1	n.4149-1553G>T		intron_variant	Intron 25 of 27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000486641.2	n.999-917G>T		intron_variant	Intron 6 of 9	1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22998 AN: 151988 Hom.: 1792 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.151 AC: 22998 AN: 152106 Hom.: 1792 Cov.: 32 AF XY: 0.149 AC XY: 11077 AN XY: 74360

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.0916

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0875 Hom.: 148

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008706; hg19: chr9-16034538;