Variant rs251177 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033449.3(FCHSD1):c.828+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,561,704 control chromosomes in the GnomAD database, including 41,789 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 0.25 ( 5430 hom., cov: 32)

Exomes 𝑓: 0.22 ( 36359 hom. )

Consequence

FCHSD1
NM_033449.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

FCHSD1 (HGNC:25463): (FCH and double SH3 domains 1) Predicted to enable lipid binding activity. Predicted to be involved in neuromuscular synaptic transmission and positive regulation of actin filament polymerization. Predicted to be located in cell projection and perikaryon. Predicted to be active in neuromuscular junction and recycling endosome. Predicted to colocalize with cuticular plate. [provided by Alliance of Genome Resources, Apr 2022]

FCHSD1 links:

FCHSD1 (HGNC:):

FCHSD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCHSD1	NM_033449.3 linkuse as main transcript	c.828+81A>G		intron_variant		ENST00000435817.7	NP_258260.1	Q86WN1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCHSD1	ENST00000435817.7 linkuse as main transcript	c.828+81A>G		intron_variant		1	NM_033449.3	ENSP00000399259.2		Q86WN1-1

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38417

AN:

151916

Hom.:

5431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.00947

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.248

GnomAD4 exome

AF:

0.222

AC:

312635

AN:

1409670

Hom.:

36359

Cov.:

AF XY:

0.220

AC XY:

153113

AN XY:

695422

show subpopulations

Gnomad4 AFR exome

AF:

0.365

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.00535

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.183

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.253

AC:

38435

AN:

152034

Hom.:

5430

Cov.:

AF XY:

0.246

AC XY:

18283

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.359

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.293

Gnomad4 EAS

AF:

0.00949

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.237

Hom.:

6108

Bravo

AF:

0.261

Asia WGS

AF:

0.0930

AC:

324

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.30

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over