rs28645201

Variant summary

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

The NM_001145065.2(CCSER1):​c.1725-20249A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 152,262 control chromosomes in the GnomAD database, including 453 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 0.040 ( 453 hom., cov: 32)

Consequence

CCSER1
NM_001145065.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.59
Variant links:
Genes affected
CCSER1 (HGNC:29349): (coiled-coil serine rich protein 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCSER1NM_001145065.2 linkuse as main transcriptc.1725-20249A>G intron_variant ENST00000509176.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCSER1ENST00000509176.6 linkuse as main transcriptc.1725-20249A>G intron_variant 1 NM_001145065.2 P1Q9C0I3-1
CCSER1ENST00000432775.6 linkuse as main transcriptc.1725-20249A>G intron_variant 1 Q9C0I3-2
CCSER1ENST00000505073.5 linkuse as main transcriptc.1725-20249A>G intron_variant, NMD_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0403
AC:
6126
AN:
152144
Hom.:
452
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0133
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.0531
Gnomad ASJ
AF:
0.0256
Gnomad EAS
AF:
0.346
Gnomad SAS
AF:
0.0309
Gnomad FIN
AF:
0.0890
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0248
Gnomad OTH
AF:
0.0476
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0402
AC:
6127
AN:
152262
Hom.:
453
Cov.:
32
AF XY:
0.0439
AC XY:
3268
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0133
Gnomad4 AMR
AF:
0.0526
Gnomad4 ASJ
AF:
0.0256
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.0311
Gnomad4 FIN
AF:
0.0890
Gnomad4 NFE
AF:
0.0248
Gnomad4 OTH
AF:
0.0480
Alfa
AF:
0.0293
Hom.:
19
Bravo
AF:
0.0396
Asia WGS
AF:
0.184
AC:
638
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.4
DANN
Benign
0.78

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.

Other links and lift over

dbSNP: rs28645201; hg19: chr4-91528927; API