rs11933531

Variant names:

• chr4-91494378-G-A
• rs11933531
• NM_001145065.2:c.2218-104194G>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.2218-104194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0885 in 151,492 control chromosomes in the GnomAD database, including 821 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 0.088 (821 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2218-104194G>A		intron_variant	Intron 10 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2218-104194G>A		intron_variant	Intron 10 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000649522.1	c.92-104194G>A		intron_variant	Intron 2 of 2			ENSP00000497818.1

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13386 AN: 151374 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0518

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0885 AC: 13407 AN: 151492 Hom.: 821 Cov.: 32 AF XY: 0.0948 AC XY: 7016 AN XY: 74036

African (AFR) AF: 0.0937 AC: 3878 AN: 41384

American (AMR) AF: 0.157 AC: 2380 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 198 AN: 3456

East Asian (EAS) AF: 0.256 AC: 1322 AN: 5158

South Asian (SAS) AF: 0.183 AC: 877 AN: 4804

European-Finnish (FIN) AF: 0.0951 AC: 1001 AN: 10530

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0518 AC: 3508 AN: 67720

Other (OTH) AF: 0.0762 AC: 160 AN: 2100

Alfa AF: 0.0687 Hom.: 1202

Bravo AF: 0.0926

Asia WGS AF: 0.220 AC: 763 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.65
PhyloP100		-0.049
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: rs11933531; hg19: chr4-92415529;