20-290584-T-TTTTTTTTA

Position:

• chr20-290584-T-TTTTTTTTA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_080571.2(C20orf96):​c.17+2_17+3insTAAAAAAA variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,554,240 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00051 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000044 (2 hom.)
• Consequence: C20orf96 NM_080571.2 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C20orf96	NM_153269.3	c.20+6_20+7insTAAAAAAA		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	c.20+6_20+7insTAAAAAAA		splice_region_variant, intron_variant		1	NM_153269.3	ENSP00000353470.2
C20orf96	ENST00000400269.4	c.17+2_17+3insTAAAAAAA		splice_donor_variant, intron_variant		1		ENSP00000383128.4

Frequencies

GnomAD3 genomes AF: 0.000510 AC: 69 AN: 135320 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000216

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000153

Gnomad OTH AF: 0.00107

GnomAD4 exome AF: 0.0000444 AC: 63 AN: 1418886 Hom.: 2 Cov.: 36 AF XY: 0.0000482 AC XY: 34 AN XY: 705106

Gnomad4 AFR exome AF: 0.000421

Gnomad4 AMR exome AF: 0.000129

Gnomad4 ASJ exome AF: 0.000119

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000369

Gnomad4 FIN exome AF: 0.0000825

Gnomad4 NFE exome AF: 0.0000266

Gnomad4 OTH exome AF: 0.000102

GnomAD4 genome AF: 0.000510 AC: 69 AN: 135354 Hom.: 0 Cov.: 0 AF XY: 0.000400 AC XY: 26 AN XY: 64952

Gnomad4 AFR AF: 0.00188

Gnomad4 AMR AF: 0.000216

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000153

Gnomad4 OTH AF: 0.00106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3835237; hg19: chr20-271225;