rs10509497

Variant names:

• chr10-84397747-A-C
• rs10509497
• NM_001284240.2:c.1615-20024A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-84397747-A-C
• chr10-84397747-A-G
• chr10-84397747-A-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.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
• Publications: 5 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CCSER2	NM_001284240.2	c.1615-20024A>C		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.1615-20024A>C		intron_variant	Intron 3 of 9	2	NM_001284240.2	ENSP00000361160.2
CCSER2	ENST00000224756.12	c.1615-20024A>C		intron_variant	Intron 3 of 10	5		ENSP00000224756.8
CCSER2	ENST00000494144.5	n.90+3805A>C		intron_variant	Intron 1 of 6	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

African (AFR) AF: 0.123 AC: 5098 AN: 41554

American (AMR) AF: 0.299 AC: 4576 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2582 AN: 5140

South Asian (SAS) AF: 0.434 AC: 2093 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5646 AN: 10558

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31961 AN: 67966

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.431 Hom.: 24279

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
PhyloP100		-0.49
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: rs10509497; hg19: chr10-86157503;