rs2141848

Variant names:

• chr4-91474205-A-C
• rs2141848
• NM_001145065.2:c.2218-124367A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-91474205-A-C
• chr4-91474205-A-G
• chr4-91474205-A-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.2218-124367A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,612 control chromosomes in the GnomAD database, including 26,456 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 (26456 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2218-124367A>C		intron_variant	Intron 10 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2218-124367A>C		intron_variant	Intron 10 of 10	1	NM_001145065.2	ENSP00000425040.1
CCSER1	ENST00000649522.1	c.92-124367A>C		intron_variant	Intron 2 of 2			ENSP00000497818.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88601 AN: 151494 Hom.: 26430 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.585 AC: 88678 AN: 151612 Hom.: 26456 Cov.: 31 AF XY: 0.589 AC XY: 43669 AN XY: 74112

African (AFR) AF: 0.647 AC: 26764 AN: 41390

American (AMR) AF: 0.561 AC: 8527 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1971 AN: 3454

East Asian (EAS) AF: 0.865 AC: 4454 AN: 5152

South Asian (SAS) AF: 0.669 AC: 3224 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5782 AN: 10518

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36259 AN: 67774

Other (OTH) AF: 0.551 AC: 1161 AN: 2106

Alfa AF: 0.451 Hom.: 1385

Bravo AF: 0.587

Asia WGS AF: 0.726 AC: 2519 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.46
PhyloP100		-0.56
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: rs2141848; hg19: chr4-92395356;