9-15586536-C-T

Variant names:

• chr9-15586536-C-T
• rs10810402
• NM_173550.4:c.353-4830C>T

Variant summary

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

The NM_001355547.1(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_001355547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 3 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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355547.1. 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.353-4830C>T		intron	N/A	NP_775821.2
	CCDC171	NM_001355547.1		c.353-4830C>T		intron	N/A	NP_001342476.1
	CCDC171	NM_001348002.2		c.-89-996C>T		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.353-4830C>T		intron	N/A	ENSP00000370077.3
	CCDC171	ENST00000905141.1		c.353-4830C>T		intron	N/A	ENSP00000575200.1
	CCDC171	ENST00000971281.1		c.353-4830C>T		intron	N/A	ENSP00000641340.1

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

African (AFR) AF: 0.240 AC: 9932 AN: 41460

American (AMR) AF: 0.450 AC: 6860 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1719 AN: 3468

East Asian (EAS) AF: 0.729 AC: 3754 AN: 5152

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5675 AN: 10526

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29446 AN: 67922

Other (OTH) AF: 0.437 AC: 920 AN: 2106

Alfa AF: 0.412 Hom.: 5756

Bravo AF: 0.391

Asia WGS AF: 0.569 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.78
PhyloP100		0.83
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: rs10810402; hg19: chr9-15586534;