chr9-15586536-C-T

Position:

• chr9-15586536-C-T

Variant summary

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

The NM_173550.4(CCDC171):​c.353-4830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,908 control chromosomes in the GnomAD database, including 13,390 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 0.40 (13390 hom., cov: 31)
• Consequence: CCDC171 NM_173550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC171	NM_173550.4	c.353-4830C>T		intron_variant		ENST00000380701.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC171	ENST00000380701.8	c.353-4830C>T		intron_variant		1	NM_173550.4	P1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61255 AN: 151790 Hom.: 13385 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.403 AC: 61284 AN: 151908 Hom.: 13390 Cov.: 31 AF XY: 0.414 AC XY: 30749 AN XY: 74220

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.437

Alfa AF: 0.418 Hom.: 3972

Bravo AF: 0.391

Asia WGS AF: 0.569 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10810402; hg19: chr9-15586534;