20-290584-T-TTTTTAA

Variant names:

• chr20-290584-T-TTTTTAA
• rs3835237
• NM_153269.3:c.20+6_20+7insTTAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_080571.2(C20orf96):​c.17+2_17+3insTTAAAA variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: C20orf96 NM_080571.2 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080571.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C20orf96	NM_153269.3	MANE Select	c.20+6_20+7insTTAAAA		splice_region intron	N/A	NP_695001.2	Q9NUD7
	C20orf96	NM_080571.2		c.17+2_17+3insTTAAAA		splice_donor intron	N/A	NP_542138.1	F5GZA9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C20orf96	ENST00000360321.7	TSL:1 MANE Select	c.20+6_20+7insTTAAAA		splice_region intron	N/A	ENSP00000353470.2	Q9NUD7
	C20orf96	ENST00000400269.4	TSL:1	c.17+2_17+3insTTAAAA		splice_donor intron	N/A	ENSP00000383128.4	F5GZA9
	C20orf96	ENST00000907056.1		c.20+6_20+7insTTAAAA		splice_region intron	N/A	ENSP00000577115.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 40

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs3835237; hg19: chr20-271225;