rs10516882

Variant names:

• chr4-90987425-C-A
• rs10516882
• NM_001145065.2:c.2172+63978C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-90987425-C-A
• chr4-90987425-C-G

Variant summary

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

The NM_001145065.2(CCSER1):​c.2172+63978C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,322 control chromosomes in the GnomAD database, including 1,680 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 0.14 (1680 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2172+63978C>A		intron_variant	Intron 9 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2172+63978C>A		intron_variant	Intron 9 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000509109.5	n.*151-27936C>A		intron_variant	Intron 6 of 9	1		ENSP00000421693.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21398 AN: 151204 Hom.: 1674 Cov.: 31

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.142 AC: 21417 AN: 151322 Hom.: 1680 Cov.: 31 AF XY: 0.142 AC XY: 10484 AN XY: 73912

African (AFR) AF: 0.0883 AC: 3650 AN: 41326

American (AMR) AF: 0.202 AC: 3048 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 667 AN: 3452

East Asian (EAS) AF: 0.168 AC: 857 AN: 5108

South Asian (SAS) AF: 0.132 AC: 635 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1149 AN: 10548

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10908 AN: 67648

Other (OTH) AF: 0.146 AC: 307 AN: 2104

Alfa AF: 0.145 Hom.: 1000

Bravo AF: 0.149

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-0.036
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: rs10516882; hg19: chr4-91908576;