rs10017262

chr4-90873670-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CCSER1 (HGNC:29349): (coiled-coil serine rich protein 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSER1	NM_001145065.2	c.2095-49700T>G		intron_variant		ENST00000509176.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER1	ENST00000509176.6	c.2095-49700T>G		intron_variant		1	NM_001145065.2	P1

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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.391

Alfa AF: 0.400 Hom.: 6790

Bravo AF: 0.426

Asia WGS AF: 0.237 AC: 821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.5
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs10017262; hg19: chr4-91794821;