chr4-91049276-C-G

Variant names:

• chr4-91049276-C-G
• rs1461588
• NM_001145065.2:c.2173-36674C>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.2173-36674C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,226 control chromosomes in the GnomAD database, including 62,491 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 0.91 (62491 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 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.2173-36674C>G		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.2173-36674C>G		intron	N/A	ENSP00000425040.1
	CCSER1	ENST00000509109.5	TSL:1	n.*431+31972C>G		intron	N/A	ENSP00000421693.1

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137655 AN: 152108 Hom.: 62436 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.905 AC: 137768 AN: 152226 Hom.: 62491 Cov.: 32 AF XY: 0.903 AC XY: 67150 AN XY: 74404

African (AFR) AF: 0.919 AC: 38190 AN: 41540

American (AMR) AF: 0.900 AC: 13757 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3002 AN: 3472

East Asian (EAS) AF: 0.914 AC: 4726 AN: 5168

South Asian (SAS) AF: 0.719 AC: 3468 AN: 4826

European-Finnish (FIN) AF: 0.926 AC: 9815 AN: 10604

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.909 AC: 61817 AN: 68010

Other (OTH) AF: 0.895 AC: 1893 AN: 2116

Alfa AF: 0.908 Hom.: 7798

Bravo AF: 0.907

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.020
DANN	Benign	0.41
PhyloP100		-2.4
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: rs1461588; hg19: chr4-91970427;