chr9-16000237-C-T

Position:

• chr9-16000237-C-T

Variant summary

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

The ENST00000486641.2(CCDC171):​n.369-20352C>T 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 0.0364 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC171	XM_017014432.3	c.3870-18066C>T		intron_variant			XP_016869921.1
CCDC171	XM_017014437.3	c.3778-22095C>T		intron_variant			XP_016869926.1
CCDC171	XR_001746227.3	n.4149-35856C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000486641.2	n.369-20352C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0615

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0231 Hom.: 9

Bravo AF: 0.0355

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79156074; hg19: chr9-16000235;