4-91082746-C-T

Variant names:

• chr4-91082746-C-T
• rs6532271
• NM_001145065.2:c.2173-3204C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145065.2(CCSER1):​c.2173-3204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,766 control chromosomes in the GnomAD database, including 3,301 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 0.20 (3301 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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.2173-3204C>T		intron	N/A	NP_001138537.1	Q9C0I3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCSER1	ENST00000509176.6	TSL:1 MANE Select	c.2173-3204C>T		intron	N/A	ENSP00000425040.1	Q9C0I3-1
	CCSER1	ENST00000509109.5	TSL:1	n.*432-3204C>T		intron	N/A	ENSP00000421693.1	D6RAM2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29793 AN: 151648 Hom.: 3294 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.197 AC: 29842 AN: 151766 Hom.: 3301 Cov.: 31 AF XY: 0.196 AC XY: 14580 AN XY: 74204

African (AFR) AF: 0.284 AC: 11740 AN: 41348

American (AMR) AF: 0.265 AC: 4048 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3466

East Asian (EAS) AF: 0.227 AC: 1166 AN: 5142

South Asian (SAS) AF: 0.107 AC: 514 AN: 4802

European-Finnish (FIN) AF: 0.114 AC: 1201 AN: 10544

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10215 AN: 67902

Other (OTH) AF: 0.180 AC: 379 AN: 2104

Alfa AF: 0.0658 Hom.: 62

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.69
PhyloP100		-1.4
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: rs6532271; hg19: chr4-92003897;