rs6849036

Positions:

• chr4-90989732-T-C

Variant summary

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

The NM_001145065.2(CCSER1):​c.2172+66285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,284 control chromosomes in the GnomAD database, including 7,673 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 0.30 (7673 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2172+66285T>C		intron_variant		ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2172+66285T>C		intron_variant		1	NM_001145065.2	ENSP00000425040	P1
CCSER1	ENST00000509109.5	c.*151-25629T>C		intron_variant, NMD_transcript_variant		1		ENSP00000421693

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45614 AN: 151168 Hom.: 7631 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.302 AC: 45714 AN: 151284 Hom.: 7673 Cov.: 31 AF XY: 0.305 AC XY: 22537 AN XY: 73926

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.269

Alfa AF: 0.237 Hom.: 6991

Bravo AF: 0.329

Asia WGS AF: 0.304 AC: 1056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.80

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: rs6849036; hg19: chr4-91910883;