chr4-90386374-A-G

Position:

• chr4-90386374-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145065.2(CCSER1):​c.1510-13662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,968 control chromosomes in the GnomAD database, including 9,669 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 0.35 (9669 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSER1	NM_001145065.2	c.1510-13662A>G		intron_variant		ENST00000509176.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSER1	ENST00000509176.6	c.1510-13662A>G		intron_variant		1	NM_001145065.2	P1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53195 AN: 151850 Hom.: 9661 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.350 AC: 53227 AN: 151968 Hom.: 9669 Cov.: 32 AF XY: 0.350 AC XY: 25989 AN XY: 74282

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.346

Alfa AF: 0.325 Hom.: 10789

Bravo AF: 0.353

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.90

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: rs2169398; hg19: chr4-91307525;