Genetic Variant :null (chr20-59479794-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

0 publications found

Variant links:

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Classification according to ACGS-UK Somatic Oncogenicity v2025

Our verdict: Likely_benign. The variant received -4 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.144 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

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

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence