rs187200046

Variant names:

• chr4-90480460-C-T
• rs187200046
• NM_001145065.2:c.1724+12106C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145065.2(CCSER1):​c.1724+12106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,586 control chromosomes in the GnomAD database, including 15,065 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 0.35 (15065 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

Genes affected

CCSER1 (HGNC:29349): (coiled-coil serine rich protein 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.1724+12106C>T		intron_variant	Intron 5 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.1724+12106C>T		intron_variant	Intron 5 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000432775.6	c.1724+12106C>T		intron_variant	Intron 5 of 7	1		ENSP00000389283.2
CCSER1	ENST00000505073.5	n.1724+12106C>T		intron_variant	Intron 5 of 9	1		ENSP00000420964.1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52733 AN: 151466 Hom.: 15021 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.349 AC: 52835 AN: 151586 Hom.: 15065 Cov.: 32 AF XY: 0.344 AC XY: 25518 AN XY: 74086

African (AFR) AF: 0.791 AC: 32595 AN: 41182

American (AMR) AF: 0.222 AC: 3378 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1903 AN: 5122

South Asian (SAS) AF: 0.190 AC: 914 AN: 4818

European-Finnish (FIN) AF: 0.198 AC: 2096 AN: 10560

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10469 AN: 67892

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.271 Hom.: 1196

Bravo AF: 0.373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.14
PhyloP100		-1.3
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: rs187200046; hg19: chr4-91401611;