rs1903575

Variant names:

• chr4-90290767-G-A
• rs1903575
• NM_001145065.2:c.-41-17477G>A

Variant summary

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

The NM_001145065.2(CCSER1):​c.-41-17477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,844 control chromosomes in the GnomAD database, including 1,628 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 0.14 (1628 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145065.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	NM_001145065.2	MANE Select	c.-41-17477G>A		intron	N/A	NP_001138537.1	Q9C0I3-1
	CCSER1	NM_001377987.1		c.-41-17477G>A		intron	N/A	NP_001364916.1
	CCSER1	NM_207491.2		c.-41-17477G>A		intron	N/A	NP_997374.1	Q9C0I3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.-41-17477G>A		intron	N/A	ENSP00000425040.1	Q9C0I3-1
	CCSER1	ENST00000432775.6	TSL:1	c.-41-17477G>A		intron	N/A	ENSP00000389283.2	Q9C0I3-2
	CCSER1	ENST00000505073.5	TSL:1	n.-41-17477G>A		intron	N/A	ENSP00000420964.1	E7EUW0

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20521 AN: 151726 Hom.: 1626 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0805

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.135 AC: 20536 AN: 151844 Hom.: 1628 Cov.: 32 AF XY: 0.135 AC XY: 9990 AN XY: 74214

African (AFR) AF: 0.203 AC: 8410 AN: 41404

American (AMR) AF: 0.0799 AC: 1215 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0805 AC: 279 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1560 AN: 5142

South Asian (SAS) AF: 0.0964 AC: 465 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10562

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6830 AN: 67932

Other (OTH) AF: 0.124 AC: 261 AN: 2102

Alfa AF: 0.109 Hom.: 267

Bravo AF: 0.134

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.65
PhyloP100		-0.52
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: rs1903575; hg19: chr4-91211918;