NM_001145065.2:c.2218-119839T>C

Variant names:

• chr4-91478733-T-C
• rs7675583
• NM_001145065.2:c.2218-119839T>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.2218-119839T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,582 control chromosomes in the GnomAD database, including 25,848 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 0.58 (25848 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	NM_001145065.2	MANE Select	c.2218-119839T>C		intron	N/A	NP_001138537.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.2218-119839T>C		intron	N/A	ENSP00000425040.1
	CCSER1	ENST00000649522.1		c.92-119839T>C		intron	N/A	ENSP00000497818.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87624 AN: 151466 Hom.: 25827 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.579 AC: 87697 AN: 151582 Hom.: 25848 Cov.: 32 AF XY: 0.583 AC XY: 43192 AN XY: 74070

African (AFR) AF: 0.623 AC: 25787 AN: 41404

American (AMR) AF: 0.559 AC: 8505 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1977 AN: 3458

East Asian (EAS) AF: 0.870 AC: 4494 AN: 5166

South Asian (SAS) AF: 0.668 AC: 3220 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5801 AN: 10532

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.535 AC: 36224 AN: 67678

Other (OTH) AF: 0.549 AC: 1155 AN: 2102

Alfa AF: 0.549 Hom.: 69652

Bravo AF: 0.580

Asia WGS AF: 0.724 AC: 2508 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.78
PhyloP100		0.011
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: rs7675583; hg19: chr4-92399884;