rs10516869

Variant names:

• chr4-90376285-G-A
• rs10516869
• NM_001145065.2:c.1510-23751G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145065.2(CCSER1):​c.1510-23751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,194 control chromosomes in the GnomAD database, including 254 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 0.048 (254 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.1510-23751G>A		intron_variant	Intron 3 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.1510-23751G>A		intron_variant	Intron 3 of 10	1	NM_001145065.2	ENSP00000425040.1

Frequencies

GnomAD3 genomes AF: 0.0476 AC: 7246 AN: 152076 Hom.: 254 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0476 AC: 7247 AN: 152194 Hom.: 254 Cov.: 32 AF XY: 0.0497 AC XY: 3702 AN XY: 74418

African (AFR) AF: 0.0369 AC: 1533 AN: 41540

American (AMR) AF: 0.0547 AC: 835 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.184 AC: 949 AN: 5170

South Asian (SAS) AF: 0.0711 AC: 343 AN: 4824

European-Finnish (FIN) AF: 0.0626 AC: 664 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0406 AC: 2759 AN: 68000

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0396 Hom.: 42

Bravo AF: 0.0465

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10516869; hg19: chr4-91297436;