chr4-90184150-C-A

Variant names:

• chr4-90184150-C-A
• rs10516865
• NM_001145065.2:c.-42+56319C>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.-42+56319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 151,852 control chromosomes in the GnomAD database, including 687 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 0.069 (687 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.-42+56319C>A		intron_variant	Intron 1 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.-42+56319C>A		intron_variant	Intron 1 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000505073.5	n.-42+56319C>A		intron_variant	Intron 1 of 9	1		ENSP00000420964.1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10470 AN: 151734 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0639

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

GnomAD4 genome AF: 0.0691 AC: 10498 AN: 151852 Hom.: 687 Cov.: 32 AF XY: 0.0672 AC XY: 4985 AN XY: 74176

African (AFR) AF: 0.172 AC: 7112 AN: 41384

American (AMR) AF: 0.0469 AC: 714 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0468 AC: 162 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5172

South Asian (SAS) AF: 0.0376 AC: 181 AN: 4810

European-Finnish (FIN) AF: 0.0163 AC: 172 AN: 10522

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1994 AN: 67954

Other (OTH) AF: 0.0632 AC: 133 AN: 2104

Alfa AF: 0.0319 Hom.: 180

Bravo AF: 0.0754

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.50
PhyloP100		0.97
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: rs10516865; hg19: chr4-91105301;