chr4-91286392-A-G

Variant names:

• chr4-91286392-A-G
• rs10516889
• NM_001145065.2:c.2217+200398A>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.2217+200398A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 151,918 control chromosomes in the GnomAD database, including 208 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 0.027 (208 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 1 publications found

Genes affected

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

LOC124900733 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2217+200398A>G		intron_variant	Intron 10 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2217+200398A>G		intron_variant	Intron 10 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000649522.1	c.91+2538A>G		intron_variant	Intron 2 of 2			ENSP00000497818.1

Frequencies

GnomAD3 genomes AF: 0.0268 AC: 4061 AN: 151800 Hom.: 208 Cov.: 32

Gnomad AFR AF: 0.00565

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0267 AC: 4061 AN: 151918 Hom.: 208 Cov.: 32 AF XY: 0.0304 AC XY: 2257 AN XY: 74230

African (AFR) AF: 0.00566 AC: 235 AN: 41544

American (AMR) AF: 0.0722 AC: 1098 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1152 AN: 5142

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4830

European-Finnish (FIN) AF: 0.0434 AC: 461 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0122 AC: 825 AN: 67800

Other (OTH) AF: 0.0280 AC: 59 AN: 2104

Alfa AF: 0.0143 Hom.: 37

Bravo AF: 0.0291

Asia WGS AF: 0.133 AC: 464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		1.1
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: rs10516889; hg19: chr4-92207543;