rs7870244

Positions:

• chr9-15755197-G-A
• chr9-15755197-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC171	NM_173550.4	c.2671+9566G>A		intron_variant		ENST00000380701.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC171	ENST00000380701.8	c.2671+9566G>A		intron_variant		1	NM_173550.4	P1
CCDC171	ENST00000449575.6	c.390+9566G>A		intron_variant		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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0497

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.00217

Gnomad4 NFE AF: 0.00630

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0221 Hom.: 92

Bravo AF: 0.0812

Asia WGS AF: 0.134 AC: 464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.58

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: rs7870244; hg19: chr9-15755195;