rs10516879

chr4-90819399-T-C

Variant summary

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

The NM_001145065.2(CCSER1):c.2094+3554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,040 control chromosomes in the GnomAD database, including 4,367 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 0.24 (4367 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSER1	NM_001145065.2	c.2094+3554T>C		intron_variant		ENST00000509176.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER1	ENST00000509176.6	c.2094+3554T>C		intron_variant		1	NM_001145065.2	P1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36082 AN: 151922 Hom.: 4364 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.237 AC: 36107 AN: 152040 Hom.: 4367 Cov.: 32 AF XY: 0.236 AC XY: 17551 AN XY: 74330

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.203

Alfa AF: 0.225 Hom.: 8101

Bravo AF: 0.237

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.1
Dann	Benign	0.75

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: rs10516879; hg19: chr4-91740550;