rs12416239

Variant names:

• chr10-116327708-A-T
• rs12416239
• NM_198515.3:c.165+2320A>T

Variant summary

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

The NM_198515.3(CCDC172):​c.165+2320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,096 control chromosomes in the GnomAD database, including 1,112 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 0.11 (1112 hom., cov: 33)
• Consequence: CCDC172 NM_198515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC172	NM_198515.3	c.165+2320A>T		intron_variant	Intron 3 of 8	ENST00000333254.4	NP_940917.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC172	ENST00000333254.4	c.165+2320A>T		intron_variant	Intron 3 of 8	1	NM_198515.3	ENSP00000329860.3
CCDC172	ENST00000497093.1	n.169+2320A>T		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16912 AN: 151976 Hom.: 1114 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.111 AC: 16935 AN: 152096 Hom.: 1112 Cov.: 33 AF XY: 0.113 AC XY: 8439 AN XY: 74364

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.0936

Gnomad4 FIN AF: 0.0833

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0932 Hom.: 96

Bravo AF: 0.123

Asia WGS AF: 0.153 AC: 526 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	16
DANN	Benign	0.59

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: rs12416239; hg19: chr10-118087220;