dbSNP rs10509497: CCSER2:c.1615-20024A>C (chr10-84397747-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Variant links:

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]

CCSER2 links:

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ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
CCSER2	NM_001284240.2 link	c.1615-20024A>C		intron_variant	Intron 3 of 9	ENST00000372088.8	NP_001271169.1	Q9H7U1-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCSER2	ENST00000372088.8 link	c.1615-20024A>C	intron_variant	Intron 3 of 9	2	NM_001284240.2	ENSP00000361160.2	Q9H7U1-3
CCSER2	ENST00000224756.12 link	c.1615-20024A>C	intron_variant	Intron 3 of 10	5		ENSP00000224756.8	Q9H7U1-1
CCSER2	ENST00000494144.5 link	n.90+3805A>C	intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54673

AN:

151984

Hom.:

11647

Cov.:

show subpopulations

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.:

AF XY:

0.364

AC XY:

27027

AN XY:

74302

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over