rs4636575

chr10-116340068-A-G

Variant summary

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

The NM_198515.3(CCDC172):c.166-666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.094 in 151,902 control chromosomes in the GnomAD database, including 925 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 0.094 (925 hom., cov: 32)
• Consequence: CCDC172 NM_198515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

CCDC172 (HGNC:30524): (coiled-coil domain containing 172) Predicted to be located in cytoplasm and sperm midpiece. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC172	NM_198515.3	c.166-666A>G		intron_variant		ENST00000333254.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC172	ENST00000333254.4	c.166-666A>G		intron_variant		1	NM_198515.3	P1
CCDC172	ENST00000497093.1	n.170-702A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14250 AN: 151782 Hom.: 928 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.0940 AC: 14275 AN: 151902 Hom.: 925 Cov.: 32 AF XY: 0.0954 AC XY: 7084 AN XY: 74272

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0636 Hom.: 179

Bravo AF: 0.107

Asia WGS AF: 0.153 AC: 532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	14
Dann	Benign	0.68

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: rs4636575; hg19: chr10-118099580;