NM_001145065.2:c.2094+3554T>C

Variant names:

• chr4-90819399-T-C
• rs10516879
• NM_001145065.2:c.2094+3554T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145065.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	NM_001145065.2	MANE Select	c.2094+3554T>C		intron	N/A	NP_001138537.1	Q9C0I3-1
	CCSER1	NM_001377987.1		c.2094+3554T>C		intron	N/A	NP_001364916.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.2094+3554T>C		intron	N/A	ENSP00000425040.1	Q9C0I3-1
	CCSER1	ENST00000505073.5	TSL:1	n.*193+3554T>C		intron	N/A	ENSP00000420964.1	E7EUW0
	CCSER1	ENST00000509109.5	TSL:1	n.153+3554T>C		intron	N/A	ENSP00000421693.1	D6RAM2

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

African (AFR) AF: 0.276 AC: 11444 AN: 41470

American (AMR) AF: 0.180 AC: 2742 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5164

South Asian (SAS) AF: 0.167 AC: 807 AN: 4824

European-Finnish (FIN) AF: 0.242 AC: 2555 AN: 10556

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15623 AN: 67964

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.230 Hom.: 16903

Bravo AF: 0.237

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
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: rs10516879; hg19: chr4-91740550;