rs11200999

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001284240.2(CCSER2):​c.-40+9972C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,064 control chromosomes in the GnomAD database, including 11,539 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 0.36 ( 11539 hom., cov: 33)

Consequence

CCSER2
NM_001284240.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.382
Variant links:
Genes affected
CCSER2 (HGNC:29197): (coiled-coil serine rich protein 2) Predicted to enable microtubule binding activity. Predicted to act upstream of or within microtubule bundle formation. Predicted to be located in cytoplasm and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCSER2NM_001284240.2 linkuse as main transcriptc.-40+9972C>G intron_variant ENST00000372088.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCSER2ENST00000372088.8 linkuse as main transcriptc.-40+9972C>G intron_variant 2 NM_001284240.2 P4Q9H7U1-3
CCSER2ENST00000359979.8 linkuse as main transcriptc.-40+9972C>G intron_variant 1 Q9H7U1-2
CCSER2ENST00000224756.12 linkuse as main transcriptc.-40+9972C>G intron_variant 5 A1Q9H7U1-1

Frequencies

GnomAD3 genomes
AF:
0.357
AC:
54185
AN:
151946
Hom.:
11544
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.114
Gnomad AMI
AF:
0.554
Gnomad AMR
AF:
0.297
Gnomad ASJ
AF:
0.372
Gnomad EAS
AF:
0.502
Gnomad SAS
AF:
0.437
Gnomad FIN
AF:
0.535
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.469
Gnomad OTH
AF:
0.372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.356
AC:
54172
AN:
152064
Hom.:
11539
Cov.:
33
AF XY:
0.361
AC XY:
26813
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.114
Gnomad4 AMR
AF:
0.297
Gnomad4 ASJ
AF:
0.372
Gnomad4 EAS
AF:
0.502
Gnomad4 SAS
AF:
0.437
Gnomad4 FIN
AF:
0.535
Gnomad4 NFE
AF:
0.469
Gnomad4 OTH
AF:
0.368
Alfa
AF:
0.407
Hom.:
1731
Bravo
AF:
0.329
Asia WGS
AF:
0.454
AC:
1581
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.5
DANN
Benign
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11200999; hg19: chr10-86098536; API