rs10509494

chr10-84393152-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.56).
• 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/exons	MANE	UniProt
CCSER2	NM_001284240.2	c.1614+19337C>T		intron_variant		ENST00000372088.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER2	ENST00000372088.8	c.1614+19337C>T		intron_variant		2	NM_001284240.2	P4
CCSER2	ENST00000224756.12	c.1614+19337C>T		intron_variant		5		A1

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

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0920 Hom.: 643

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

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: rs10509494; hg19: chr10-86152908;