Variant 20-290584-T-TTTTA 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+7insTAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 1,472,022 control chromosomes in the GnomAD database, including 1,164 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.084 ( 749 hom., cov: 0)

Exomes 𝑓: 0.031 ( 415 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

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 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+7insTAAA		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+7insTAAA		splice_region_variant, intron_variant		1	NM_153269.3	ENSP00000353470	P1
C20orf96	ENST00000400269.4 linkuse as main transcript	c.17+2_17+3insTAAA		splice_region_variant, intron_variant		1		ENSP00000383128

Frequencies

GnomAD3 genomes

AF:

0.0840

AC:

11339

AN:

134992

Hom.:

747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.00903

Gnomad AMR

AF:

0.0541

Gnomad ASJ

AF:

0.0581

Gnomad EAS

AF:

0.0316

Gnomad SAS

AF:

0.0882

Gnomad FIN

AF:

0.0213

Gnomad MID

AF:

0.0567

Gnomad NFE

AF:

0.0701

Gnomad OTH

AF:

0.0699

GnomAD3 exomes

AF:

0.0262

AC:

4451

AN:

170000

Hom.:

479

AF XY:

0.0256

AC XY:

2387

AN XY:

93350

show subpopulations

Gnomad AFR exome

AF:

0.0472

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0239

Gnomad EAS exome

AF:

0.0179

Gnomad SAS exome

AF:

0.0274

Gnomad FIN exome

AF:

0.0280

Gnomad NFE exome

AF:

0.0259

Gnomad OTH exome

AF:

0.0274

GnomAD4 exome

AF:

0.0312

AC:

41718

AN:

1336994

Hom.:

415

Cov.:

AF XY:

0.0304

AC XY:

20195

AN XY:

663756

show subpopulations

Gnomad4 AFR exome

AF:

0.0703

Gnomad4 AMR exome

AF:

0.0153

Gnomad4 ASJ exome

AF:

0.0221

Gnomad4 EAS exome

AF:

0.0144

Gnomad4 SAS exome

AF:

0.0335

Gnomad4 FIN exome

AF:

0.0216

Gnomad4 NFE exome

AF:

0.0319

Gnomad4 OTH exome

AF:

0.0308

GnomAD4 genome

AF:

0.0840

AC:

11347

AN:

135028

Hom.:

749

Cov.:

AF XY:

0.0806

AC XY:

5224

AN XY:

64810

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.0540

Gnomad4 ASJ

AF:

0.0581

Gnomad4 EAS

AF:

0.0313

Gnomad4 SAS

AF:

0.0880

Gnomad4 FIN

AF:

0.0213

Gnomad4 NFE

AF:

0.0702

Gnomad4 OTH

AF:

0.0694

Alfa

AF:

0.0242

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