NM_001145065.2:c.2095-49700T>G

Variant names:

• chr4-90873670-T-G
• rs10017262
• NM_001145065.2:c.2095-49700T>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.2095-49700T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,948 control chromosomes in the GnomAD database, including 13,923 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 0.42 (13923 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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.2095-49700T>G		intron	N/A	NP_001138537.1
	CCSER1	NM_001377987.1		c.2095-49700T>G		intron	N/A	NP_001364916.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.2095-49700T>G		intron	N/A	ENSP00000425040.1
	CCSER1	ENST00000505073.5	TSL:1	n.*194-49700T>G		intron	N/A	ENSP00000420964.1
	CCSER1	ENST00000509109.5	TSL:1	n.154-37585T>G		intron	N/A	ENSP00000421693.1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63277 AN: 151830 Hom.: 13902 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.417 AC: 63339 AN: 151948 Hom.: 13923 Cov.: 32 AF XY: 0.409 AC XY: 30387 AN XY: 74262

African (AFR) AF: 0.548 AC: 22727 AN: 41452

American (AMR) AF: 0.350 AC: 5339 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5156

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4822

European-Finnish (FIN) AF: 0.351 AC: 3707 AN: 10562

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27105 AN: 67924

Other (OTH) AF: 0.391 AC: 824 AN: 2108

Alfa AF: 0.403 Hom.: 9222

Bravo AF: 0.426

Asia WGS AF: 0.237 AC: 821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.082
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: rs10017262; hg19: chr4-91794821;