rs513522

Positions:

• chr20-271524-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153269.3(C20orf96):​c.1032-257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,902 control chromosomes in the GnomAD database, including 10,991 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 0.36 (10991 hom., cov: 31)
• Consequence: C20orf96 NM_153269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C20orf96	NM_153269.3	c.1032-257T>C		intron_variant		ENST00000360321.7	NP_695001.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C20orf96	ENST00000360321.7	c.1032-257T>C		intron_variant		1	NM_153269.3	ENSP00000353470	P1
C20orf96	ENST00000400269.4	c.1029-257T>C		intron_variant		1		ENSP00000383128
C20orf96	ENST00000382369.9	c.927-257T>C		intron_variant		5		ENSP00000371806

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53940 AN: 151784 Hom.: 10951 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.356 AC: 54048 AN: 151902 Hom.: 10991 Cov.: 31 AF XY: 0.354 AC XY: 26303 AN XY: 74228

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.378

Alfa AF: 0.292 Hom.: 9287

Bravo AF: 0.362

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.62
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs513522; hg19: chr20-252165;