rs513522

Variant names:

• chr20-271524-A-G
• rs513522
• NM_153269.3:c.1032-257T>C

Variant summary

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

The NM_153269.3(C20orf96):​c.1032-257T>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
• Publications: 5 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=-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 rank	MANE	Protein	UniProt
C20orf96	NM_153269.3	c.1032-257T>C		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.1032-257T>C		intron_variant	Intron 10 of 10	1	NM_153269.3	ENSP00000353470.2
C20orf96	ENST00000400269.4	c.1029-257T>C		intron_variant	Intron 10 of 10	1		ENSP00000383128.4
C20orf96	ENST00000382369.9	c.927-257T>C		intron_variant	Intron 8 of 8	5		ENSP00000371806.5

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

African (AFR) AF: 0.570 AC: 23579 AN: 41366

American (AMR) AF: 0.276 AC: 4222 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1282 AN: 5150

South Asian (SAS) AF: 0.379 AC: 1822 AN: 4810

European-Finnish (FIN) AF: 0.273 AC: 2882 AN: 10548

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17800 AN: 67968

Other (OTH) AF: 0.378 AC: 796 AN: 2106

Alfa AF: 0.299 Hom.: 12474

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
PhyloP100		-0.38
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: rs513522; hg19: chr20-252165;