4-90646872-T-G

Variant names:

• chr4-90646872-T-G
• rs12505502
• NM_001145065.2:c.1932+18640T>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.1932+18640T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,880 control chromosomes in the GnomAD database, including 13,136 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 0.41 (13136 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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.1932+18640T>G		intron	N/A	NP_001138537.1	Q9C0I3-1
	CCSER1	NM_001377987.1		c.1932+18640T>G		intron	N/A	NP_001364916.1
	CCSER1	NM_207491.2		c.1932+18640T>G		intron	N/A	NP_997374.1	Q9C0I3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.1932+18640T>G		intron	N/A	ENSP00000425040.1	Q9C0I3-1
	CCSER1	ENST00000432775.6	TSL:1	c.1932+18640T>G		intron	N/A	ENSP00000389283.2	Q9C0I3-2
	CCSER1	ENST00000505073.5	TSL:1	n.1933-16973T>G		intron	N/A	ENSP00000420964.1	E7EUW0

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62111 AN: 151762 Hom.: 13132 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.409 AC: 62146 AN: 151880 Hom.: 13136 Cov.: 31 AF XY: 0.403 AC XY: 29936 AN XY: 74218

African (AFR) AF: 0.381 AC: 15758 AN: 41370

American (AMR) AF: 0.382 AC: 5818 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1643 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1281 AN: 5144

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3695 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30897 AN: 67952

Other (OTH) AF: 0.431 AC: 906 AN: 2102

Alfa AF: 0.420 Hom.: 11356

Bravo AF: 0.413

Asia WGS AF: 0.307 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.74
PhyloP100		-1.9
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: rs12505502; hg19: chr4-91568023;