NM_198515.3:c.165+2320A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38

Publications

1 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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
CCDC172NM_198515.3 linkc.165+2320A>T intron_variant Intron 3 of 8 ENST00000333254.4 NP_940917.1 P0C7W6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC172ENST00000333254.4 linkc.165+2320A>T intron_variant Intron 3 of 8 1 NM_198515.3 ENSP00000329860.3 P0C7W6
CCDC172ENST00000497093.1 linkn.169+2320A>T intron_variant Intron 2 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.111
AC:
16912
AN:
151976
Hom.:
1114
Cov.:
33
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.165
AC:
6836
AN:
41514
American (AMR)
AF:
0.164
AC:
2501
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.0766
AC:
266
AN:
3472
East Asian (EAS)
AF:
0.215
AC:
1108
AN:
5158
South Asian (SAS)
AF:
0.0936
AC:
452
AN:
4830
European-Finnish (FIN)
AF:
0.0833
AC:
884
AN:
10612
Middle Eastern (MID)
AF:
0.130
AC:
38
AN:
292
European-Non Finnish (NFE)
AF:
0.0659
AC:
4473
AN:
67926
Other (OTH)
AF:
0.121
AC:
255
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
760
1520
2279
3039
3799
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
180
360
540
720
900
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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
PhyloP100
1.4
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

Publications

Other links and lift over

dbSNP: rs12416239; hg19: chr10-118087220; API