4-90290767-G-A

Position:

• chr4-90290767-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.-41-17477G>A		intron_variant		ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.-41-17477G>A		intron_variant		1	NM_001145065.2	ENSP00000425040	P1
CCSER1	ENST00000432775.6	c.-41-17477G>A		intron_variant		1		ENSP00000389283
CCSER1	ENST00000505073.5	c.-41-17477G>A		intron_variant, NMD_transcript_variant		1		ENSP00000420964

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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.0805

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.0964

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.124

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs1903575; hg19: chr4-91211918;