20-272080-A-T

Variant names:

• chr20-272080-A-T
• rs8117711
• NM_153269.3:c.1032-813T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153269.3(C20orf96):​c.1032-813T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,360 control chromosomes in the GnomAD database, including 897 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (897 hom., cov: 32)
• Consequence: C20orf96 NM_153269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C20orf96	NM_153269.3	c.1032-813T>A		intron_variant	Intron 10 of 10	ENST00000360321.7	NP_695001.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C20orf96	ENST00000360321.7	c.1032-813T>A		intron_variant	Intron 10 of 10	1	NM_153269.3	ENSP00000353470.2
C20orf96	ENST00000400269.4	c.1029-813T>A		intron_variant	Intron 10 of 10	1		ENSP00000383128.4
C20orf96	ENST00000382369.9	c.927-813T>A		intron_variant	Intron 8 of 8	5		ENSP00000371806.5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16345 AN: 151246 Hom.: 894 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.134

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16361 AN: 151360 Hom.: 897 Cov.: 32 AF XY: 0.110 AC XY: 8123 AN XY: 73952

African (AFR) AF: 0.0825 AC: 3374 AN: 40906

American (AMR) AF: 0.0943 AC: 1435 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3464

East Asian (EAS) AF: 0.164 AC: 846 AN: 5162

South Asian (SAS) AF: 0.159 AC: 760 AN: 4772

European-Finnish (FIN) AF: 0.117 AC: 1238 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7635 AN: 67988

Other (OTH) AF: 0.139 AC: 292 AN: 2098

Alfa AF: 0.102 Hom.: 100

Bravo AF: 0.106

Asia WGS AF: 0.206 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.084
DANN	Benign	0.084
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8117711; hg19: chr20-252721; COSMIC: COSV100826899; COSMIC: COSV100826899;