chr20-290584-T-TTTTTTTA

Position:

• chr20-290584-T-TTTTTTTA

Variant summary

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

The NM_153269.3(C20orf96):​c.20+6_20+7insTAAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000448 in 1,553,294 control chromosomes in the GnomAD database, including 13 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0018 (2 hom., cov: 0)
  • Exomes 𝑓: 0.00032 (11 hom.)
• Consequence: C20orf96 NM_153269.3 splice_region, 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 GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C20orf96	NM_153269.3	c.20+6_20+7insTAAAAAA		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+7insTAAAAAA		splice_region_variant, intron_variant		1	NM_153269.3	ENSP00000353470	P1
C20orf96	ENST00000400269.4	c.17+2_17+3insTAAAAAA		splice_region_variant, intron_variant		1		ENSP00000383128

Frequencies

GnomAD3 genomes AF: 0.00182 AC: 246 AN: 135310 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000864

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000229

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000276

Gnomad OTH AF: 0.00215

GnomAD4 exome AF: 0.000317 AC: 449 AN: 1417952 Hom.: 11 Cov.: 36 AF XY: 0.000299 AC XY: 211 AN XY: 704668

Gnomad4 AFR exome AF: 0.00326

Gnomad4 AMR exome AF: 0.000387

Gnomad4 ASJ exome AF: 0.000238

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000357

Gnomad4 FIN exome AF: 0.000206

Gnomad4 NFE exome AF: 0.000239

Gnomad4 OTH exome AF: 0.000478

GnomAD4 genome AF: 0.00183 AC: 247 AN: 135342 Hom.: 2 Cov.: 0 AF XY: 0.00186 AC XY: 121 AN XY: 64950

Gnomad4 AFR AF: 0.00632

Gnomad4 AMR AF: 0.000864

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000230

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000276

Gnomad4 OTH AF: 0.00213

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;