chr9-15634328-T-C

Variant names:

• chr9-15634328-T-C
• rs4740619
• NM_173550.4:c.822+10915T>C

Variant summary

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

The NM_173550.4(CCDC171):​c.822+10915T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,844 control chromosomes in the GnomAD database, including 18,139 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 0.48 (18139 hom., cov: 32)
• Consequence: CCDC171 NM_173550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 83 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173550.4. 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
	CCDC171	NM_173550.4	MANE Select	c.822+10915T>C		intron	N/A	NP_775821.2
	CCDC171	NM_001355547.1		c.822+10915T>C		intron	N/A	NP_001342476.1
	CCDC171	NM_001348002.2		c.543+10915T>C		intron	N/A	NP_001334931.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC171	ENST00000380701.8	TSL:1 MANE Select	c.822+10915T>C		intron	N/A	ENSP00000370077.3

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73304 AN: 151726 Hom.: 18124 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.483 AC: 73359 AN: 151844 Hom.: 18139 Cov.: 32 AF XY: 0.493 AC XY: 36604 AN XY: 74220

African (AFR) AF: 0.449 AC: 18613 AN: 41426

American (AMR) AF: 0.586 AC: 8936 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3915 AN: 5136

South Asian (SAS) AF: 0.550 AC: 2651 AN: 4816

European-Finnish (FIN) AF: 0.544 AC: 5705 AN: 10486

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30390 AN: 67940

Other (OTH) AF: 0.504 AC: 1062 AN: 2108

Alfa AF: 0.466 Hom.: 46217

Bravo AF: 0.488

Asia WGS AF: 0.599 AC: 2084 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.85
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4740619; hg19: chr9-15634326;