chr4-90996265-A-G

Position:

• chr4-90996265-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145065.2(CCSER1):​c.2172+72818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,976 control chromosomes in the GnomAD database, including 6,887 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 0.27 (6887 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2172+72818A>G		intron_variant		ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2172+72818A>G		intron_variant		1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000509109.5	n.*151-19096A>G		intron_variant		1		ENSP00000421693.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41562 AN: 151856 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.273 AC: 41554 AN: 151976 Hom.: 6887 Cov.: 32 AF XY: 0.274 AC XY: 20346 AN XY: 74250

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.309

Alfa AF: 0.346 Hom.: 15162

Bravo AF: 0.257

Asia WGS AF: 0.317 AC: 1096 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.41

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: rs2035116; hg19: chr4-91917416;