rs2141848

chr4-91474205-A-Cchr4-91474205-A-Gchr4-91474205-A-T

Variant summary

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

The NM_001145065.2(CCSER1):c.2218-124367A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,612 control chromosomes in the GnomAD database, including 26,456 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 0.58 (26456 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSER1	NM_001145065.2	c.2218-124367A>C		intron_variant		ENST00000509176.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER1	ENST00000509176.6	c.2218-124367A>C		intron_variant		1	NM_001145065.2	P1
CCSER1	ENST00000649522.1	c.92-124367A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88601 AN: 151494 Hom.: 26430 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.585 AC: 88678 AN: 151612 Hom.: 26456 Cov.: 31 AF XY: 0.589 AC XY: 43669 AN XY: 74112

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.551

Alfa AF: 0.438 Hom.: 1241

Bravo AF: 0.587

Asia WGS AF: 0.726 AC: 2519 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.60
Dann	Benign	0.46

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: rs2141848; hg19: chr4-92395356;