4-91429191-C-T

Position:

• chr4-91429191-C-T

Variant summary

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

The NM_001145065.2(CCSER1):​c.2218-169381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,548 control chromosomes in the GnomAD database, including 21,756 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 0.53 (21756 hom., cov: 32)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2218-169381C>T		intron_variant		ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2218-169381C>T		intron_variant		1	NM_001145065.2	ENSP00000425040	P1
CCSER1	ENST00000649522.1	c.91+145337C>T		intron_variant				ENSP00000497818

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80170 AN: 151430 Hom.: 21742 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.529 AC: 80216 AN: 151548 Hom.: 21756 Cov.: 32 AF XY: 0.536 AC XY: 39721 AN XY: 74048

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.507

Alfa AF: 0.546 Hom.: 22025

Bravo AF: 0.517

Asia WGS AF: 0.680 AC: 2348 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.67

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: rs6845679; hg19: chr4-92350342;