20-59479794-G-A

Variant names:

• chr20-59479794-G-A
• rs1592272

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The variant 20-59479794-G-A has been identified. The variant allele was found at a cumulative frequency of 0.00991 (AC=1,510) in the gnomAD database across 152,314 control chromosomes, including 76 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.144. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0099 (76 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 0 publications found

Classification according to ACMG Germline Pathogenicity v2019

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

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.1439 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.00995	AC:1514	Hom:77	AN:152196	Cov:33
GnomAD4 genome	AF: 0.00991	AC:1510	Hom:76	AN:152314	Cov:33
TOPMed (Bravo)	AF: 0.0122	AC:3234	Hom:206	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00372	AC:205	Hom:5	AN:55170	Cov:
Local & regional cohorts 8 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.00769	AC:18	Hom:3	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.193	AC:	Hom:	AN:	Cov:
GenomeAsia100K	AF: 0.0570	AC:199	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.177	AC:1282	Hom:	AN:7234	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.145	AC:17747	Hom:1288	AN:122782	Cov:
Turkish Variome	AF: 0.00647	AC:10	Hom:0	AN:1546	Cov:
UK10K	AF: 0.000397	AC:3	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.175	AC:1569	Hom:132	AN:8960	Cov:

Showing 12 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.8
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.44
GPN-Star LLR	N/A	-0.19
GPN-Star score	N/A	-0.18
PhyloP100	Benign	-1.8

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1592272;

hg19: chr20-58054849;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar