chr9-15755197-G-A

Variant names:

• chr9-15755197-G-A
• rs7870244
• NM_173550.4:c.2671+9566G>A

Variant summary

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

The NM_173550.4(CCDC171):​c.2671+9566G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,134 control chromosomes in the GnomAD database, including 1,023 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 0.074 (1023 hom., cov: 32)
• Consequence: CCDC171 NM_173550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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.2671+9566G>A		intron	N/A	NP_775821.2
	CCDC171	NM_001355547.1		c.2695+9566G>A		intron	N/A	NP_001342476.1
	CCDC171	NM_001348002.2		c.2416+9566G>A		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.2671+9566G>A		intron	N/A	ENSP00000370077.3
	CCDC171	ENST00000449575.6	TSL:2	c.388+9566G>A		intron	N/A	ENSP00000409055.2

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11194 AN: 152016 Hom.: 999 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00629

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0740 AC: 11254 AN: 152134 Hom.: 1023 Cov.: 32 AF XY: 0.0743 AC XY: 5530 AN XY: 74388

African (AFR) AF: 0.206 AC: 8531 AN: 41474

American (AMR) AF: 0.0497 AC: 759 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.112 AC: 582 AN: 5176

South Asian (SAS) AF: 0.123 AC: 592 AN: 4822

European-Finnish (FIN) AF: 0.00217 AC: 23 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.00630 AC: 428 AN: 67988

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0237 Hom.: 117

Bravo AF: 0.0812

Asia WGS AF: 0.134 AC: 464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.060
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: rs7870244; hg19: chr9-15755195;