rs10516865

chr4-90184150-C-Achr4-90184150-C-T

Variant summary

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

The NM_001145065.2(CCSER1):c.-42+56319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 151,852 control chromosomes in the GnomAD database, including 687 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 0.069 (687 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSER1	NM_001145065.2	c.-42+56319C>A		intron_variant		ENST00000509176.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER1	ENST00000509176.6	c.-42+56319C>A		intron_variant		1	NM_001145065.2	P1
CCSER1	ENST00000505073.5	c.-42+56319C>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10470 AN: 151734 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0639

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

GnomAD4 genome AF: 0.0691 AC: 10498 AN: 151852 Hom.: 687 Cov.: 32 AF XY: 0.0672 AC XY: 4985 AN XY: 74176

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0468

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0376

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0293

Gnomad4 OTH AF: 0.0632

Alfa AF: 0.0129 Hom.: 15

Bravo AF: 0.0754

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.50

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: rs10516865; hg19: chr4-91105301;