rs3835237

chr20-290584-T-TTAchr20-290584-T-TTTAchr20-290584-T-TTTTAchr20-290584-T-TTTTTAchr20-290584-T-TTTTTAAchr20-290584-T-TTTTTTAchr20-290584-T-TTTTTTTAchr20-290584-T-TTTTTTTTAchr20-290584-T-TTTTTTTTTAchr20-290584-T-TTTTTTTTTTA

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
• 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 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	UniProt
C20orf96	NM_153269.3	c.20+6_20+7insTA		splice_region_variant, intron_variant		ENST00000360321.7

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 2231 AN: 135278 Hom.: 52 Cov.: 0

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

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.: 36 AF XY: 0.0663 AC XY: 42728 AN XY: 644620

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.: 54 Cov.: 0 AF XY: 0.0164 AC XY: 1066 AN XY: 64926

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.: 40

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;