rs10509497

chr10-84397747-A-Cchr10-84397747-A-Gchr10-84397747-A-T

Variant summary

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

The NM_001284240.2(CCSER2):c.1615-20024A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,102 control chromosomes in the GnomAD database, including 11,643 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 (11643 hom., cov: 33)
• Consequence: CCSER2 NM_001284240.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

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=-0.91).
• 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.1615-20024A>C		intron_variant		ENST00000372088.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER2	ENST00000372088.8	c.1615-20024A>C		intron_variant		2	NM_001284240.2	P4
CCSER2	ENST00000224756.12	c.1615-20024A>C		intron_variant		5		A1
CCSER2	ENST00000494144.5	n.90+3805A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54673 AN: 151984 Hom.: 11647 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.359 AC: 54660 AN: 152102 Hom.: 11643 Cov.: 33 AF XY: 0.364 AC XY: 27027 AN XY: 74302

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.370

Alfa AF: 0.444 Hom.: 19805

Bravo AF: 0.333

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.53
Dann	Benign	0.71

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: rs10509497; hg19: chr10-86157503;