rs10509494

Variant names:

• chr10-84393152-C-T
• rs10509494
• NM_001284240.2:c.1614+19337C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001284240.2(CCSER2):​c.1614+19337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,144 control chromosomes in the GnomAD database, including 513 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 0.077 (513 hom., cov: 31)
• Consequence: CCSER2 NM_001284240.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 2 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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER2	NM_001284240.2	c.1614+19337C>T		intron_variant	Intron 3 of 9	ENST00000372088.8	NP_001271169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER2	ENST00000372088.8	c.1614+19337C>T		intron_variant	Intron 3 of 9	2	NM_001284240.2	ENSP00000361160.2
CCSER2	ENST00000224756.12	c.1614+19337C>T		intron_variant	Intron 3 of 10	5		ENSP00000224756.8

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11732 AN: 152026 Hom.: 511 Cov.: 31

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0237

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0771 AC: 11737 AN: 152144 Hom.: 513 Cov.: 31 AF XY: 0.0747 AC XY: 5557 AN XY: 74392

African (AFR) AF: 0.0626 AC: 2599 AN: 41510

American (AMR) AF: 0.0818 AC: 1251 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4814

European-Finnish (FIN) AF: 0.0650 AC: 687 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6404 AN: 68002

Other (OTH) AF: 0.0903 AC: 190 AN: 2104

Alfa AF: 0.0906 Hom.: 791

Bravo AF: 0.0787

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.58
PhyloP100		1.2
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: rs10509494; hg19: chr10-86152908;