10-84338780-C-G

Variant names:

• chr10-84338780-C-G
• rs11200999
• NM_001284240.2:c.-40+9972C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284240.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER2	NM_001284240.2	MANE Select	c.-40+9972C>G		intron	N/A	NP_001271169.1
	CCSER2	NM_001351290.2		c.-40+9972C>G		intron	N/A	NP_001338219.1
	CCSER2	NM_001351292.2		c.-40+9972C>G		intron	N/A	NP_001338221.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER2	ENST00000372088.8	TSL:2 MANE Select	c.-40+9972C>G		intron	N/A	ENSP00000361160.2
	CCSER2	ENST00000359979.8	TSL:1	c.-40+9972C>G		intron	N/A	ENSP00000353068.4
	CCSER2	ENST00000224756.12	TSL:5	c.-40+9972C>G		intron	N/A	ENSP00000224756.8

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

African (AFR) AF: 0.114 AC: 4731 AN: 41482

American (AMR) AF: 0.297 AC: 4537 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3464

East Asian (EAS) AF: 0.502 AC: 2600 AN: 5180

South Asian (SAS) AF: 0.437 AC: 2111 AN: 4830

European-Finnish (FIN) AF: 0.535 AC: 5634 AN: 10538

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31855 AN: 67990

Other (OTH) AF: 0.368 AC: 776 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.47
PhyloP100		0.38
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

Other links and lift over

dbSNP: rs11200999; hg19: chr10-86098536;