chr10-111282335-T-G

Variant names:

• chr10-111282335-T-G
• rs10885122

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 10-111282335-T-G has been identified. The variant allele was found at a cumulative frequency of 0.715 (AC=108,759) in the gnomAD database across 152,040 control chromosomes, including 43,396 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.91. 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 0.72 (43396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 104 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 = 0.91 — 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: 0.716	AC:108744	Hom:43393	AN:151922	Cov:31
GnomAD4 genome	AF: 0.715	AC:108759	Hom:43396	AN:152040	Cov:31
TOPMed (Bravo)	AF: 0.697	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.823	AC:583692	Hom:249561	AN:708948	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.772	AC:1809	Hom:713	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.922	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.863	AC:259	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.804	AC:2797	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.905	AC:6542	Hom:	AN:7230	Cov:
Qatari Genome	AF: 0.676	AC:119	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.909	AC:111636	Hom:50741	AN:122826	Cov:
Turkish Variome	AF: 0.860	AC:1330	Hom:572	AN:1546	Cov:
UK10K	AF: 0.869	AC:6575	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.934	AC:8366	Hom:3900	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	4.3
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.66
GPN-Star LLR	N/A	0.67
GPN-Star score	N/A	-0.67
PhyloP100	Benign	-0.31

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: rs10885122;

hg19: chr10-113042093;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar