rs11200999

chr10-84338780-C-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

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]

ACMG classification

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
CCSER2	NM_001284240.2	c.-40+9972C>G		intron_variant		ENST00000372088.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER2	ENST00000372088.8	c.-40+9972C>G		intron_variant		2	NM_001284240.2	P4
CCSER2	ENST00000359979.8	c.-40+9972C>G		intron_variant		1
CCSER2	ENST00000224756.12	c.-40+9972C>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54185 AN: 151946 Hom.: 11544 Cov.: 33

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

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

Other links and lift over

dbSNP: rs11200999; hg19: chr10-86098536;