Variant rs3835237 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_153269.3(C20orf96):c.20+6_20+7insTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 1,432,950 control chromosomes in the GnomAD database, including 1,200 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.017 ( 54 hom., cov: 0)

Exomes 𝑓: 0.067 ( 1146 hom. )

Consequence

C20orf96
NM_153269.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.380

Variant links:

Genes affected

C20orf96 (HGNC:16227): (chromosome 20 open reading frame 96)

C20orf96 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C20orf96	NM_153269.3 linkuse as main transcript	c.20+6_20+7insTA		splice_region_variant, intron_variant		ENST00000360321.7	NP_695001.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C20orf96	ENST00000360321.7 linkuse as main transcript	c.20+6_20+7insTA		splice_region_variant, intron_variant		1	NM_153269.3	ENSP00000353470	P1
C20orf96	ENST00000400269.4 linkuse as main transcript	c.17+2_17+3insTA		splice_region_variant, intron_variant		1		ENSP00000383128

Frequencies

GnomAD3 genomes

AF:

0.0165

AC:

2231

AN:

135278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0305

Gnomad AMI

AF:

0.0135

Gnomad AMR

AF:

0.0115

Gnomad ASJ

AF:

0.0178

Gnomad EAS

AF:

0.00610

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.0137

Gnomad MID

AF:

0.0176

Gnomad NFE

AF:

0.0121

Gnomad OTH

AF:

0.0166

GnomAD3 exomes

AF:

0.0668

AC:

11353

AN:

170000

Hom.:

1659

AF XY:

0.0676

AC XY:

6307

AN XY:

93350

show subpopulations

Gnomad AFR exome

AF:

0.0438

Gnomad AMR exome

AF:

0.0590

Gnomad ASJ exome

AF:

0.0619

Gnomad EAS exome

AF:

0.0736

Gnomad SAS exome

AF:

0.0550

Gnomad FIN exome

AF:

0.0820

Gnomad NFE exome

AF:

0.0726

Gnomad OTH exome

AF:

0.0555

GnomAD4 exome

AF:

0.0668

AC:

86708

AN:

1297638

Hom.:

1146

Cov.:

AF XY:

0.0663

AC XY:

42728

AN XY:

644620

show subpopulations

Gnomad4 AFR exome

AF:

0.0376

Gnomad4 AMR exome

AF:

0.0505

Gnomad4 ASJ exome

AF:

0.0514

Gnomad4 EAS exome

AF:

0.0865

Gnomad4 SAS exome

AF:

0.0490

Gnomad4 FIN exome

AF:

0.0746

Gnomad4 NFE exome

AF:

0.0693

Gnomad4 OTH exome

AF:

0.0626

GnomAD4 genome

AF:

0.0165

AC:

2236

AN:

135312

Hom.:

Cov.:

AF XY:

0.0164

AC XY:

1066

AN XY:

64926

show subpopulations

Gnomad4 AFR

AF:

0.0304

Gnomad4 AMR

AF:

0.0115

Gnomad4 ASJ

AF:

0.0178

Gnomad4 EAS

AF:

0.00612

Gnomad4 SAS

AF:

0.00666

Gnomad4 FIN

AF:

0.0137

Gnomad4 NFE

AF:

0.0121

Gnomad4 OTH

AF:

0.0176

Alfa

AF:

0.0414

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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