4-90386374-A-G

Variant names:

• chr4-90386374-A-G
• rs2169398
• NM_001145065.2:c.1510-13662A>G

Variant summary

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

The NM_001145065.2(CCSER1):​c.1510-13662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,968 control chromosomes in the GnomAD database, including 9,669 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 (9669 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	NM_001145065.2	MANE Select	c.1510-13662A>G		intron	N/A	NP_001138537.1
	CCSER1	NM_001377987.1		c.1510-13662A>G		intron	N/A	NP_001364916.1
	CCSER1	NM_207491.2		c.1510-13662A>G		intron	N/A	NP_997374.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.1510-13662A>G		intron	N/A	ENSP00000425040.1
	CCSER1	ENST00000432775.6	TSL:1	c.1510-13662A>G		intron	N/A	ENSP00000389283.2
	CCSER1	ENST00000505073.5	TSL:1	n.1510-13662A>G		intron	N/A	ENSP00000420964.1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53195 AN: 151850 Hom.: 9661 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.350 AC: 53227 AN: 151968 Hom.: 9669 Cov.: 32 AF XY: 0.350 AC XY: 25989 AN XY: 74282

African (AFR) AF: 0.422 AC: 17491 AN: 41426

American (AMR) AF: 0.330 AC: 5043 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1628 AN: 5146

South Asian (SAS) AF: 0.440 AC: 2119 AN: 4816

European-Finnish (FIN) AF: 0.275 AC: 2910 AN: 10576

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21563 AN: 67942

Other (OTH) AF: 0.346 AC: 733 AN: 2116

Alfa AF: 0.329 Hom.: 13998

Bravo AF: 0.353

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.90
PhyloP100		0.27
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: rs2169398; hg19: chr4-91307525;