9-16000237-C-T

Variant names:

• chr9-16000237-C-T
• rs79156074
• ENST00000486641.2:n.369-20352C>T

Variant summary

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

The ENST00000486641.2(CCDC171):​n.369-20352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 152,184 control chromosomes in the GnomAD database, including 153 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 0.036 (153 hom., cov: 32)
• Consequence: CCDC171 ENST00000486641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0599 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC171	ENST00000486641.2	TSL:1	n.369-20352C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0365 AC: 5543 AN: 152066 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0364 AC: 5546 AN: 152184 Hom.: 153 Cov.: 32 AF XY: 0.0331 AC XY: 2464 AN XY: 74418

African (AFR) AF: 0.0103 AC: 426 AN: 41532

American (AMR) AF: 0.0261 AC: 399 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4814

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10606

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0615 AC: 4178 AN: 67988

Other (OTH) AF: 0.0294 AC: 62 AN: 2108

Alfa AF: 0.0315 Hom.: 72

Bravo AF: 0.0355

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.58
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs79156074; hg19: chr9-16000235;