chr16-56951227-A-G

Variant names:

• chr16-56951227-A-G
• rs9989419

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The variant 16-56951227-A-G has been identified. The variant allele was found at a cumulative frequency of 0.56 (AC=85,096) in the gnomAD database across 151,990 control chromosomes, including 24,656 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.741. 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 0.56 (24656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 113 publications found

Classification according to ACGS-UK Somatic Oncogenicity v2025

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

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 = 0.741 — 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: 0.560	AC:85044	Hom:24637	AN:151872	Cov:31
GnomAD4 genome	AF: 0.560	AC:85096	Hom:24656	AN:151990	Cov:31
TOPMed (Bravo)	AF: 0.553	AC:146289	Hom:41964	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.595	AC:353324	Hom:106898	AN:594024	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.583	AC:1365	Hom:415	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.754	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.537	AC:161	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.692	AC:2406	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.728	AC:5266	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.648	AC:114	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.757	AC:92869	Hom:35182	AN:122600	Cov:
Turkish Variome	AF: 0.676	AC:1045	Hom:362	AN:1546	Cov:
UK10K	AF: 0.613	AC:4638	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.760	AC:6813	Hom:2584	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.40
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.57
GPN-Star LLR	N/A	2.7
GPN-Star score	N/A	-1.4
PhyloP100	Benign	-0.76

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.

Other links and lift over

dbSNP: rs9989419;

hg19: chr16-56985139;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar